After this new batch of updates i’m looking at coming back to Xert as my primary training app. Am I right in thinking that the TrainingTime required as shown in Xert still includes all the coffee stops I make on my outdoor rides?
Yes, unfortunately 
It does. I’d look at that a little differently though. Xert is trying to model the effect of the training, and if you’re call it one ride, including the coffee stop, that break is huge rest period. Not including it would make the ride look like something it wasn’t.
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I also think this approach is the right. Some of the athletes I follow will record the commutes to and from work as one ride each day on Strava. That will of course give you very strange numbers when you look at average speeds, durations or powers, but I think it is better if they split up the rides in this case. And also hide it from the Strava feed! 
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I understand why Xert does it but it makes the “Time required to Train Field” a bit useless for me. I know I could stop and start the rides but that’s a pain and as you said I’d really need to make my Strava feed private.
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The could choose to make this and option and show moving time instead. And perhaps have a threshold for how long breaks you will have to take before it stops counting. That way all the stops you take while waiting for a green light will still be included in your ride time, while it will exclude your coffee stops etc.
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Exactly my thoughts.
On the other hand maybe I’m an outlier and everybody else who uses Xert is a more dedicated athlete and never stops for coffee.
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Or they just end the activity (home to coffee shop) and start a new one (coffee shop to home) when they ride on. I’ve always done that anyway, I never thought of that as one ride but always as two or more on one day with stops for coffee or lunch or a bath in a lake or whatever else one might want to do on a tour besides riding. It’s still training but in several parts stretched out with other stuff in between.
Just another way of looking at it though, not to invalidate your request for a ‘moving time’ option. But form a training standpoint the stop is rest and thus a factor. MPA goes up and that needs to be tracked and thus the stop can’t be just cut out and MPA left where it was before the stop. So I see why Xert does it the way they do. If you start a new activity it assumes you to be fully recovered with MPA at PP and that’s probably true after a coffee stop and it might not be true after a stop at a red light and ‘moving time’ usually cuts those out as well.
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Moving time is an old-school metric that needs to die. 
Blame the culprit. Auto-pause should have a setting to stop/end an activity after X minutes of no movement and zero cadence. I’d probably use a cut-off time of 10 minutes (full cooldown recovery).
Another option would be stop/resume logic like Strava works for commutes, but that is a distorted representation of what occurred strain-wise.
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I always turn off auto stop as it just destroys any metric. The worst examples of this are runners who do e.g. 10 x 800 m with full rest. They basically say that they can run 8 km at a much higher pace than what is actually the case.
I personally have a case where one of my longer endurance rides (165 km) includes a 25 min ferry in the middle of the ride. If I press pause, my total km and speed will be wrong as I get the ferry crossing for free. If I pause, my Garmin will stop the time, not just the recording, and my average power metrics will be a bit too high. And making it two rides is not ideals, because I end up with two shorter rides (obviously I am not fully recovered when starting on the second leg).