At this moment, there is no way for Premiere/after effects to do anything but stretch what is between the protected regions of a mogrt.
The only workaround is to offer a slider/input to the template into which you can manually enter the new total duration of the stretched clip in seconds, and then use that value in some calculations to “do clever stuff” so the wiggle does work at the correct speed.
so if the original comp is 6 seconds, with a protected intro and outro of both a second, then that leaves 4 seconds in the middle.
If you stretch out the clip to be 10 seconds, the intro and outro play at 100% speed, the middle part becomes slowed down to exactly 50%, so if the mogrt can “know” that, it could be programmed to wiggle twice as fast inbetween, and the endresult in premiere is that it wiggles at constant speed.
But the only way the mogrt can know its new length, is if you tell it, via a slider, and unfortunately, through a manual steting by the editor.