"Yet there isn't really any evidence of active crystals being located anywhere else
, either. If they are in the very heart of the reactor in TNG and ENT, and in TOS "Elaan of Troyius" and the like this seems to be true as well, why assume they would occupy a radically different location in the machinery of other eras?"
I'm not saying they're not. I'm saying they could be, given the evidence I've already cited (eg the reactor rooms in Treks II & IV). As you've correctly noted, the TMP refit Enterprise was a radically new design using the latest advances. It is therefore entirely possible that the warp system may have deviated significantly from existing designs.
I must admit - I haven't seen any of Enterprise at all, so can't comment on what was seen on that show or how it relates to subsequent designs
Re the saucer warp engines - I thought the whole point of warp nacelles being located away from the hull of the ship was so that there was a reasonable distance between the crew and the warp field? If there are warp engines located within the body of the saucer itself then that would invalidate that design element. And it also must be noted that (as far as I know) there has never been, in any Trek iteration, any mention of saucer warp engines. Trevanian's notion of introducing deployable nacelles is an extremely neat one and would have solved this conundrum at a stroke. Shame they didn't go with it - and if they told him the saucer couldn't go to warp, then they hadn't been paying enough attention to their own show.
Saquist - that's a fair theory (and an appealing one actually - I've often wondered how 'reverse impulse' works when there are no impulse engines on the bow of the saucer), but it must be noted that whatever Memory Alpha insists, it's the creation of fans, and not canon. The purpose of the crystal (if it is one) remains hazy.