I have a Mk1.5, and there is no flex when I do up the Maxle, the wheel just slots in and out. The clearance between the disc and the calliper looks normal as I recall, and I don’t think the Maxle protrudes at the thread end when tight.
I’m not near the bike so can’t offer you any measurements, but it sounds like you may be missing some sort of hub spacer.
I have the standard DT Swiss E1900 wheelset.