I'm not quite sure I follow this, but let me explain a few things about how the built-in functions work before we dive back in to scripts.
Stop - this has the quantization problem we've been talking about so we'll keep using the StopNow script instead
Overdub - this is a "toggle" function, it turns overdub on and off. Once turned on, it usually but not always stays on after other mode changes, for example you can go in and out of Mute mode and Overdub will be where it was when you started Mute.
Play - this is the universal "cancel everything I am doing and return the loop to just simple playback". It is a bit different than Play on a tapedeck because it WILL cancel Overdub mode if it is on. It will also get you out of Replace, Multiply, Loop Switch, or any other events you might have scheduled.
Pause - this is also a toggle function, it will pause the loop if it is moving, and resume the loop if it is paused
Once you have entered Pause mode after using Pause, Stop, or the StopNow script, you need a way to resume the loop playing. Pause will do that. Play will do that, but it will also cancel Overdub mode. There is also the Start function which will restart the loop from the beginning but will leave Overdub alone. Since you are already at the beginning when using Stop, then Start and Pause will behave the same way.
"Play-Mode -> StopNow -> You have to press TWO times a pedal to start again (first press: title changes from track sync to overdub track sync master, 2nd press: title changes to track sync master -> Loop plays again
Overdub-Mode -> StopNow -> You have to press ONE time a pedal to start again (first press: title changes from overdub track sync master to track sync master -> Loop plays again"
Are you describing what you ARE seeing, or is this the way you WANT it to behave?
If this is what you are seeing, what function are you using after StopNow? If it is Start, I don't see this at all.
If this is what you want to happen, then we can script it. But I'm not sure you need that. Use Start instead of Play, and I assume you already have Overdub assigned to a different switch so you can turn that on and off independently without needing a double-tap script.