Looks like you’re aware of the complexities of the WTV format and XBox extenders issues with it.
The good news if you’re willing to experiment MCEBuddy can find a way out for you.
For examples, you can write a custom profile to process the file with handbrake instead of ffmpeg. So it would something like this:
order=handbrake
handbrake-video=XXX
handbrake-audio=XXX
handbrake-audioAC3=XXX
handbrake-ext=.mp4
handbrake-remuxto=.wtv
This would make handbrake process the file and then finally remux from mp4 to wtv using ffmpeg
There are more options available including adding custom framerates to the ffmpeg profile, adding framerates to the remux section in your mcebuddy.conf file etc, check out the advanced settings topic for more details