Is ALogTime != PH hard to prove (and unknown)?
Not sure why Fortnow says there's "no meaningful model where $L$ and $NP$ collapse"... it seems to me that QBF should make them collapse, under the usual Ruzzo-Simon-Tompa oracle model (and the link you included agrees). Note this oracle model also has its quirks: we have $L = NL$ if and only if $L^A = NL^A$ for every oracle $A$, so any oracle witnessing a separation would imply the unrelativized separation.

ALogTime = LOGTIME-Uniform $NC1$. So yes, $ALogTime = NP$ is open. There is a relativized notion of uniform $NC1$, and you can collapse $NP$ and $NC1$ under that notion. See Theorem 6 in http://link.springer.com/article/10.1007/BF01692056. 
(A caveat: technically speaking, that paper considers LOGSPACE-uniform NC1, but I believe some reasonable version of that oracle construction should work in the LOGTIME-uniform setting.)

Beyond that, I know of no particular reason to believe it is "hard to prove" other than the observation that many people have tried and none have succeeded yet.