Body mount sets so many door adjustments. Not just the #2 and 3 mounts (front and rear of door).
Think of the body as 2 boxes. Engine compartment with body mounts #1 and 2, and the bed with body mounts #3 and 4.
As you move the #1 body mount it pivots on #2 and will change how the door fits to the rocker and the striker. Yes, that far away.
Usually #2 collapses a bit, that lowers the A-pillar. The engine bay box drops a little, the door now rubs the sill and sits low on the striker. The mistake is often to try and shim the hinge instead of the body mount. This screws up the Door to fender and door to windshield gaps.
Hinge alignment should be used to adjust the front of the door, not the back. Body mounts adjust the back of the door to the opening.
It is a huge game. shims here, there an stuff moves around. One gap opens, another closes, taper goes straight.
Now for the flushness. Lower hinge needs to go in. You are not moving the bed side. Maybe the upper comes out some as well. the upper window frame you just put a little body english into it to straighten into place at the very end. The fender bolts allow the fender to be loosened and moved around until they line up.