I don't know if it's typical but on my TAF the back legs are fixed slightly higher up than the TZ that I have sat next to it. As a result I had to put an oak board approx 3/4" thick under the back legs so that the cabinet & backbox would be the same height across both machines. I don't know if that means my TZ is too high, or TAF is too shallow, but the leg holes are definitely not identical.

How does one ensure that the bolts the playfield sits on inside the machine are in the right place? Perhaps that's the problem in the OP's case?

OP - get some photos of how it is mounted inside of the machine.

Post some photos of the playfield, particularly towards the back of the machine, and the hooks at the front.

Off the top of my head the gap between the top of the chair and the glass sounds about right.