I like the idea for an entrenched PaK 43 as part of the specialized Defensive commander, so it can survive the occasional artillery barrage or off-map unlike its unprotected sibling. However I think this emplacement version should then lose the ability to shoot through sightblockers and garrissons for balance reasons. Players would have to choose between survivability and firepower.
Yeah, you won't be able to upgrade to an emplacement anyhow if near a structure since it will clip through it and generally really look weird.
So in an urban environment you'd normally place the Pak 43 behind a shot blocker.
In an open field you'd be better off upgrading it with an emplacement to add to it's survivability.
It also be a nice touch if the OKW could get it as well.