It's not the end of the world if the lams aren't completely flat, if you had a maple neck blank and you slice it down the middle to make 2 bookmatched outer laminates, if there is any bowing, just align them so the hump is in the middle. When you're glueing up lots of pieces, be mindful of the laminates slipping under the clamps, it's really easy for that to happen, especially if you've got veneers between the lams, so it's worth making everything oversized, just in case.
The most awkward thing I found with lams was getting the neck blank perfectly flat and square again after glue up, easier if you've got a joiner, but it's wise to knock off the high spots with a hand plane before jointing/thicknessing, because while you will end up with a square piece of wood, it's easy for the strips in the middle to go off square with the sides/top of the neck blank.
As for alternating grain. If you've bookmatched a piece of maple and put in a wenge centre strip, you shouldn't really need to do any flipping, the wenge piece should counter any movement from the maple.
Laminates make the most stable necks IMO, I just prefer using one piece 1. it's much less work, 2, the people that will be ordering them have it in their heads that one piece is better.