No, they won't.
I had no problems at all with 2 rooms and I was the lead guest in both.
No one else in my family has a
MDE account so I didn't even bother trying to trick the system with other names.
I booked 1 room, me as the lead, checked out
Booked another room, me as the lead and checked out again.
One trip I even had 2 rooms at 2 different resorts for 1 night (long story)
No rooms or reservations were ever dropped, canceled or in any way a problem.
I've done it multiple times
The only thing that happened at check in was I had to choose which room my MB opened. I won't open 2 rooms.