I’m not an expert at all but I didn’t even notice those notches near the puzzle joint when I put my bulkhead in so I’m guessing mine wasn’t completely flush with the tape/shell. Given that you’ll be gluing the bulkhead to the shell with thickened epoxy my opinion is that the notch doesn’t really matter (gap or not) other than to help you line up and make sure the bulkhead is seated properly.
One thing to look at, which I didn’t realize until later in the build, is that the floor panels have two notches in them on the outside edge to receive the feet of the bulkhead (the two small ends now sticking up in the air). You’ll want to make sure you seat the bulkhead so those feet are even on both sides and aligned with the stitch holes. You only have about an 1/8th of inch forward and back on those feet.
From your second picture it looks like the foot on the left is higher than the foot on the right. You may want to sand the notch, or the entire left edge, to get that to sit evenly across the two sides. The feet won’t be even with the bottom of the shell (the part now in the air) but should be set back evenly to allow the floor to drop into the notches on the shell.
-mike