Sorry for the delay, I've been out traveling last week. So, full disclosure, if you're completely new to Mobius you will likely find it to be pretty....dense, might be one word. There isn't a lot of documentation and it's mostly being used by those with some prior experience. I think we can get to where you want to go, but it will take a few conversations.
A quick stab...
"The goal for me would be a base loop in 1 synced (host or transport), and then all other loops following that guy."
Assuming you are starting with b45 or below. If you tried b46 it's slightly different.
Start with a fresh session. In Default Parameters set Sync Source to Track and Track Sync Unit to Loop.
In the Tracks tab, select your first track, go to the Sync page and click on the Sync Source and Sync Unit parameter names so they turn from grey to orange. This creates what is called a parameter override. Now set Sync Source value to Transport or Host and Sync Unit to Bar.
That one track will then always sync with the host, and the other tracks will sync with the "track sync master" which is the first track recorded.
"Other tracks are quantized multiples of the base loop, so if the base loop is 4 bars, others can be 1, 2, 4, 8 etc bars but not 3. The 1/2 may be a tougher ask than 4/8 but I’d at least like to figure out how to set up the quantize and press buttons to reliably record 4 bars. I have often been getting 5 when I try."
This is a little trickier. When you have TrackSyncUnit=Loop you will always record some multiple of the loop length, but you can't restrict it to just even multiples, or powers of 2. It's based on the time you press that second Record. It will round off the recording to a loop multiple, but you have to time it right.
There are ways you can use Auto Record to pre-select the multiples you want. Use the AutoRecord function instead of Record and set Auto Record Units to 2 or 4 or 8. But you would have to set that up ahead of time and can't change your mind on the fly. Example: Track 1 sync with the host, track 2 auto records 2 loops of that, track 3 records 4 loops, track 4 records 8 loops, etc.
Kind of an in between approach is to use Auto Record with units set to 2. Then after recording starts if you press Auto Record again, each time it adds another 2 units, so you can do 2,4,6,8 but you can't skip over 6.
Scripts can be smarter about this, but it gets more complex to set up.
"A global ability to pause or mute everything and play everything. No need for individual pause that desyncs"
There are two functions GlobalPause and GlobalMute that may be enough for your needs.
If the loops are running along with something audible that the host is playing, you'll probably want GlobalMute since any form of Pause will put the loop out of alignment with the host.
"the ability to switch loop on track 2+ and maintain original alignment with base loop on 1."
This could have a few different interpretations. The key parameter here is Switch Location which should be set to Follow. What that does is try to maintain the same playback location in the new loop that was in the previous one. It's not really maintaining alignment with the host, or another track, it's just trying to keep you in the same place within the current track. And assumes you're swapping between track loops that already exist and are the same size (or an even multiple).
If track 1 is considered the master track, and you do things in other tracks (like loop switch) that put it out of alignment with the master, then this is more of a realignment problem. The Realign function should do that, but it's been undergoing quite a lot of change recently. It's also not an automatic part of loop switch. Before I dive into some options there, let's talk more about what the tracks look like and what you're trying to achieve.
"Bonus would be the ability to switch to a different base loop on 1 of the same number of bars and not break quantization. Maybe this has to be done with a dummy loop that never gets edited on 1 and all other tracks are flexible?"
Going to need more discussion. Assuming you're on b45 or earlier, "quantization" is something that happens inside a track, you can schedule something to happen on the next subcycle, cycle, or loop end point. It isn't related to things happening outside the track. So changing loops in your master track won't impact quantization in the secondary track, though it could impact Realign.
"I also haven’t figured out binding midi switches to controls, is there a learn function or do you manually assign?"
From the Bindings menu select Manage. The popup window has three areas. On the left is a table for managing "binding sets". Don't worry about that yet. In the middle is a tree where you can browse for the function you want to bind. There is a non-obvious search area above that where you can type in a name to filter the tree. On the right is a table with the current bindings. There are three tabs for *MIDI, Key, or Host Parameter bindings, make sure MIDI is selected. To create a binding, click-drag a function name from the tree onto the table. A binding editor popup should appear. For MIDI bindings you can manually enter the type, channel, and message number, or if you check the Capture box, it will listen for MIDI events that come in from the controller, and auto-select the right values. That's the closest we have to "MIDI learn" right now. Be sure to click Ok and Save on your way out of any popup windows.
"When I click a track the text goes green-red, what does that mean?"
This is a relatively obscure feature called focus lock. I won't go into that unless you want to know, but if you weren't intending to use it, then the track number (or name if you set one) should always be green. When you click directly on the number/name it toggles focus lock on and off. When focus lock is on the number is red.
If you want to select a track (move the white box) without accidentally turning focus lock on, click anywhere other than the number or the "loop stack" rectangles. It's a little touchy and needs to be improved. I usually use keyboard bindings where left/right arrow does a NextTrack and PrevTrack rather than using the mouse. I think those bindings are included with the installation package.
"in a DAW, can mobius broadcast individual tracks to different channels? MIDI on 1 routes to daw track A, MIDI on 2 to DAW B, etc?"
If you're talking about Mobius MIDI tracks recording and sending MIDI events, first of all, welcome and thanks, because I don't think many are doing much with MIDI tracks yet. What you can do with those will depend on the host. In a normal configuration, a plugin only gets one "port" where it sends all outbound MIDI events. You then have to use host routing to connect that to other things in the host that can receive MIDI. Some hosts can do filtering based on the MIDI channel of those events, others don't. Ableton for example I'm pretty sure ignores channels when routing MIDI between plugins.
If what you wanted instead was to route audio from Mobius audio tracks into different locations in the DAW, that is far more common, and I'll explain how that works.