Well, the interior design of the E-D Captain's Yacht appears to have been intended to be that of an E-D standard cabin set... Now that
doesn't tell us anything about the capabilities of the Yacht!
Also, the aeroshuttle design is purely conjectural; the outline we see resembles Starfleet's fightercraft more than its runabout. We never get a glimpse that would allow us to associate the shape with the runabout set.
In any case, the only relevant design criterion of the Delta Flyer at the time of its construction was the ability to survive great external fluid pressure. Standard shuttles apparently couldn't do it, nor could the Voyager
herself, so there's no real reason to think that a random craft sized between those two would be a suitable substitute for the building of the Delta Flyer.