A while back I made a post about an interior designer which purpose would primarily be to have a custom interior layout for the shooter adjacent gameplay. However, this could dovetail into the op’s suggestion by allowing the positioning of extra ship parts into the hull space during construction.
You wouldn’t be able to repackage the ship, and it would show up with an asterisk next to the name of the ship model you’re using, like so: DefaultShipHull in the overview and Dscan. This could also allow for player ship builder corporations to come into being.
Maybe once the walking in station stuff comes online, the corp offices could have some shops to sell specialized equipment like this.