There are quite a few benefits of how current Starship has been designed and actually nicely demonstrates how cleverly though out the whole thing is!
It goes between two places with at least some sort of atmosphere by default (or one with and on without for the Lunar variant) so while indeed dragging aerosurfaces with your in the vacuum of space might seem wasteful on the first look, you can save huge amounts of delta-v once you arrive at your destination due to atmospheric braking.
A purely built for space vacuum only craft could be built to be much lighter but would also need to loose all that excess interplanetary speed with engine power alone, potentially negating the advantages quite a bit.
There are, of course, various hybrid approaches:
- the space only craft still could have some limited aerodynamics to do earocapture to orbit at the destination or at least do aerobraking from a "cheap" eccentric capture orbit
- you could have a space only "hotel" ship on a cycler orbit and get passengers and cargo using Starship like "taxi" ships from a planet
- a big complex space-only ship could have fancy high tech low thrust & high ISP engines that would not realistically fit on craft that needs to be fairly aerodynamic
Also as for in space construction - indeed, it will enable really massive and efficient space structures, but we are not there yet space infrastructure wise. And Starships so far have shown how easily they can be made in their current form using very basic tech during their assembly, even compared to tech used for existing decades old expandable rockets! :)
So no doubt eventually big efficient high tech in space cruisers will carry the most interplanetary traffic, it seems like Starship is a surprisingly good fit for the time being & for putting in place the building stones of that future. :)