That's sort of a fallacious argument though because you could say the same thing about every part of a spacecraft that is used only for the return phase of its mission.

It might be more accurate to say that the ratio of mass for re-entry equipment to the entire craft mass is too great.

But with that said I think that the ultimate failure of the shuttle was that the design wasn't amenable to low cost maintenance. A spacecraft could have a crappy payload to orbit as long as it's cheap to maintain and use with quick turnaround.

I have a feeling that should Starship succeed this will be the case with it and it will end up having a substantially lower payload than intended but will make up for it with a design that's cheap to build and maintain.

It's not fallacious at all. Look at the difference in the hardware bringing the Apollo crews back vs Shuttle crews. Several orders of magnitude.