While travelling with my sister who is in a wheelchair and does not transfer, we had FP for MSEP and Fantasmic.
For MSEP, the FP area is in the HUB in the same place that they have FOF FP seating I believe. For starters, they would not let you in the area or even line up to get in the area before the time stated on the FP. This caused a HUGE jam of people when they finally opened the area because then people are coming from all directions (both sides, front, and behind, and wanting to be let in the FP seating area). The good things are that there was more room in general (we had enough room to sit at the curb and put our legs out) and you don't have to get there way in advance to get a spot. However, there are no spaces reserved for wheelchairs (there are spots they had marked on the pavement, but I asked and was told those are reserved for CMs to guard the area). Therefore, there is no guarantee that you won't be in the back of the area and someone will stand in front of you. However, I have found that most times when people don't have to fight for a spot to begin with, they are more accommodating for others.
For Fantasmic with the FP, it was fantastic. I don't know how it works if you don't have a FP, because I've only seen it once. They took all of the people in WC who had FP and took them in front of the rope (where the other FP were held until they were let in). There were several CMs that stood there with everyone. When they had finished cleaning up (we went to the second Fantasmic), they took us to the seats. They have seats in the top row and seats in the very first row for WC. Knowing this, when we were standing with the CMs, we requested to be in the front row (we were the only ones who did so prior to them opening the seating up for everyone (at which point everyone else filled in the bottom row). We were seated and had sent someone back to get refreshments prior to them letting others in.