I've always been the same way...take 'em all off at once. I like to meticulously clean and oil the fingerboard, as well as polish the body/pickguard where the strings were (as well as the rest of the thing). On my twelve-string acoustic (guitar) and bolt-on necks (especially the Fender Strats) the neck and/or action/intonation don't always stay static. The type of hardware that Fender and Gibson use for action and/or intonation relies on the tension of the strings to hold the settings...even tape hasn't help to ensure the settings hold when the strings are removed. Yes, I've tried marking the set-screws first in one fashion or another, usually with unsatifactory results.
My arch-top jazz box has forced the change to one-at-a-time, though. Besides the stresses on the top and neck, the ebony bridge is 'floating' (i.e., not pinned or attached to the top in any way) and the only way to adjust intonation is to physically move the bridge to/fro/aft. To remove all the strings would be maddening with regards to an action/intonation reset. Yes, I could mark the bridge position, but am reticent to do so as it is a delicate lacquer natural finish, and I just paid a bunch of $$$ to have chips/scratches filled in. There is a mark left in the lacquer on the top where the factory did their set-up and was revealed when my guy did his set (he re-levels the frets, polishes them and the fingerboard and mods the nut and bridge saddles until the action and intonation are perfect via Conn strobe). I leave the total all-at-once string removal to my yearly re-set by my Luthier.
Having said all that, I'd imagine a set-neck or neck-through Alembic, with that locking hardware, would be much less impervious to an action/intonation/neck height change than other brands, unless you have a particularly active/sensitive neck (sorry, dwmark) or play with extremely low action (a la Alembic's factory set-up). Joey, being the self set-up zen master that he is, should be the de-facto std. on this, so I trust his word when he says no problem.
FWIW, assuming the neck and action have remained static, my advice is to ALWAYS spot-ck your intonation when changing strings. Even identical strings from the same manufacturer can vary, nevermind identical guages from other manufacturers.