u are right about the clutch idea except the mainshaft is touching the flywheel where the pilot bearing goes, theres no pilot bearing on H+F series flywheels but both surfaces are machined. so no the mainshaft still maintains "some negligeable" rotation from the flywheel. i always found i had to let the clutch in, rev it and then clutch it again before getting into first.

this seems to affect preludes only from what ive heard. as far as why, dont ask why because it affects 99%+ of 1992+ preludes, so its either a 10 year design flaw or an engineered outcome. I put my money on the latter.

Having taken my tranny apart several times now (last time was late NOV), i dont see any obvious internal reason why.
If i had to guess tho, i would say it has something to do with the design of the 5th/R shift fork and how that plays with the first gear and the reverse idler gear, because reverse is 1st gear synchro hub+reverse idler gear. The reverse shift "fork" if u can call it that is this odd L shaped thing that forces the reverse idler gear into place. At the same time the 5th/R synchro sleeve locks to the end of the mainshaft on this "fake" synchro ring.
Which causes the counter shaft to spin backwards since there is an extra gear between the main and counter shafts now. The reverse idler hear engaging is also responsible for that loud clunk whenever you throw it into reverse.

~kris