Here's how I did mine:
The door sits "proud" of the sidewall by 1/8". This left room for a 3/16" seal around the t-molding on the outside of the door. It also left room for the same seal on the interior. I never put on the interior seal because the exterior seal worked well and didn't leak.
Part of the door discussion should include consideration of the type hinge you'll use.
I used strap hinges. To get the 1/8" offset, I put a 1/8" spacer under the sidewall side of the hinge. Also, I used t-molding on all sides of the doors including the hinge side. If you're going to use t-molding on the hinge side, you'll need to have the hinge centerline outside of the outer edge of the t-molding or the door won't open.