Yes, it does in a way. The MSD...
Isn't painted on the side of the ship, and isn't accurate even at face value. Nor is it INTENDED to be, for that matter.
What does the literal side of the ship have anything to do with it?
Because the dimensions and scale of the physical/CG models in relation to a fictional real-world spacecraft are presently being discussed, and the size of this can be determined, or estimated, or just plain invented, based on external visual cues. The MSDs, while interesting, are intended to be used as filming props and set decoration and are barely (if at all) useful in this regard.
Neither should they be expected to be entirely accurate in engineering terms, either.
Most such displays only resemble the vehicle to which they belong to make them easily recognizeable (this is the IN-UNIVERSE reason why MSDs look the way they do). But the shape and size of the display tells you nothing about the relation or physical location of those systems, because that's not the information they're supposed to convey.
Why isn't the MSD accurate at face value?
For starters, because at the scale of which it was drawn neither of the ship's shuttlecraft models would actually fit inside the hull, and neither would its escape pods.
More to the point: Dexler's MSD wasn't based on any specific knowledge of Defiant's actual design (as he wasn't involved in the design of the model at all) it was really just a reasonable guess to create a visual prop that would look good on TV.
even if there are contradictions in the show, and why wouldn't he intend it to be accurate as far as he can make it?
He DID, actually, considering how little information he actually had about the model. OTOH, I again remind you that physical accuracy as far as deck height and internal arrangement is not something you would expect to see even in REAL WORLD displays of this type, as that information would be virtually useless in a tabletop two-dimensional chart. A damage control floorplan or an electrical/plumbing diagram would be another matter entirely, but that's not what an MSD is, or even resembles, or was even meant to be interpreted.
He could've changed a lot for the deck plans but didn't.
That's kinda my point:
MSDs are not deckplans.