At the end of the day, the delta flyer in the first place was an excuse to do the "space race" thing with the Malon to capture that space probe they lost.
They could have done that with a claustrophobic "special space batysphere", though, for even greater dramatic effect. But they really wanted a big generic secondary craft for future storylines, as separating and stranding part of the cast is always a good driving force for drama.
I agree that if they had chosen to declare in this episode "Hey, we have this special craft here that is especially good for atmospheric operations - let's dust it off!" and then proceeded to refurbish the thing at the bottom of the forward hull, there would have been major upsides.
It would have been a sudden burst of forward-looking continuity, really: it would establish that the ship has some limited-use hardware aboard that was never quite brought to active status, so the heroes could in the future activate further special hardware the same way as needed. It would also perfectly allow for Tom Paris to insert his "Chaotica" strokes. And while it would require shooting of new type of miniature footage of the Voyager
flying without the craft in place, it would OTOH free them from building all-new sets because the runabout ones would be available in full. (Any shots of the craft undocking or redocking would not be "extra" work, as they would merely be the counterparts of the shots of the DF flying in and out of the shuttlebay.)