I don't think there is anything resembling standardization in boats - after all, they don't need to fit in anywhere. Except perhaps on trailers if that's their gig, but there's no particular "step" in the boat size continuum at standard road or railroad gauge. Boats exist primarily for the limitless seas... And, perhaps more imortantly, there always has to exist a size ever-so-slightly bigger than the preceding one so that the customer can keep up with the Joneses.
Shuttlebays in Trek don't appear standardized, either. The one in TOS is way too big for the shuttles of TOS, and would be fine for the DS9 runabouts. The one in ENT is snug for the particular auxiliaries of that ship, but for that very reason useless for most ENT auxiliaries. Etc.
Timo Saloniemi