I thought I read a while back that after submitting your TP Room res, you should not do something (can’t remember what) with MDE mobile check in.
I’m guessing you still do MDE mobile check in but NOT request any room preferences through the MDE mobile check in.
Am I making any sense?
Makes perfect sense. And yes you can still do MDE check in, but don’t put anything in the room preference that wouldn’t fit with your TP request. If that makes sense.
I usually just make sure my MDE general requests don’t conflict with room type booked nor TP room request.
I would strongly suggest you don’t put anything in the location when doing on-line check-in.
Whatever you select there gets put into the “special request” field on your reservation.
The TP request gets copied and pasted into the same field.
Therefore there is a very strong chance whichever is done last will overwrite the previous one. I could see the drop box selection being automatically added, whereas the TP one will have to be manually added.
Which means …
If you do on-line check-in first, you should be OK as long as the two don’t contradict. 
If the TP request gets added first, the online will almost certainly over-write it. No bueno. 
Edited to clarify this is my suggestion.