You make some very good points, Wingsley. Putting the torpedo launcher in the neck seems a vulnerability in retrospect, even though I know it was Jefferies' intention as far back as the Phase II design. I wish he were around to answer the question as to why, but perhaps Mr. Probert might pop in and share his thoughts on it?
Also, putting everything in one hull as in the Miranda does seem to go backwards from the idea of putting the engines and dangerous bits at a safe distance. Did Miranda crews just have to pray their warp cores never breached? The torpedoes seem like the least of the concerns there.
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Puttng it at the BASE of the neck makes more sense than putting it in a lower saucer deck. The antimatter feed conduits for "loading" the warhead have less distance to travel in the TMP configuration, and remain entirely within the secondary hulls protective mass, as opposed to snaking through the thin area of the "neck".
As for "clearance" for the torpedoes, it could no more "hit it's own ship" than the TOS version, which ALSO had to clear the saucer first.
You do make a good point, but I don't see how it's that much harder to run a line into the saucer bottom.