We bought a sovereign
with a rear bath and middle twin beds with the idea that we would flip the bedroom to the back with a queen bed, and make the bath a streetside in the middle. Weeeellllll, we did some mock-ups with cardboard of bed, toilet, etc. and ended up deciding NOT to move the bathroom after all. I couldn't get around the hatches mostly being unusable space with the set up we were going to use. And, we would lose most of our storage and closet space, as far as we could figure.
So, my suggestion is to do some mockups and play with them. We used measurements from our current SOB trailer for bed size, closet depths, counters, etc. to help us. And we went to the local Airstream dealership and walked through their trailers on the lot for more ideas. We are going to put a double bed in place of the twin on the curb side in the middle, and then build closets on the street side across from it. All our exterior hatches will still be functional this way, and we will get the storage we want. Some things are definitely still in flux and probably will be until we start to build furniture for the inside.
I know some people put the blackwater tank on top of the floor. Then you wouldn't have to worry about how to do it. I don't think the toilet could be in a different location from the blackwater tank since there's not enough water flush to really flush solids down a pipe. Unless, of course, you're one of those "pee only" people. (don't start THAT conflict again!