I don't think it is as black and white as stated here. I have experimented quite a bit with various super telelenses, using them with and without the internal filter for durations to get a thourough impression on how these filters affect performance, for the better or the worse.
I find that they have a noticeable influence on things like color balance, color casting and on fine detail rendering with high resolution cameras. The lower the resolution of the sensor, the less impact will be noticeable.
The filter is a flat piece of glass, and I believe that it is common knowledge that flat glass surfaces are relatively hard for light to travel through without being impacted, rounded surfaces are much easier.
But theory is one thing, trying it out for longer than just one shoot is much better. I owned the Canon 400mm f4DO II, and that lens had the older Canon drop-in filter glass, and the lens performed much better i.m.o. without the filter on ther high resolution 7DII. On the other hand, I also owned the Sigma 500mm f4, and that lens performed noticeably worse without the filter on the D500.
My impression is, that the better the glass coatings, like the ultra high quality coatings on the Canon 400DOII, and the worse the filter glass, the more it is likely that the lens will do better without the filter.
If the coatings are not quite top notch, leading to a lens with (slightlly lower (micro) contrast and less pure color rendering) and the filter is relatively high quality, then you may get something like with the Sigma 500S, where contrast was worse without the filter in place, and the colors and fine detail did not gain anything like with the Canon 400DOII.
The precise lens design may also play a part, but I got the feeling that it is mostly about the quality of the glass/coatings in the lens relative to the quality of the filter.
The best results though, are when there is no drop in filter in the design. Note that lenses without such a drop in filter tend to score very high, for instance:
-Nikon 500PF
-Olympus 150-400mm f4.5
-Sony 200-600mm G
These are all modern lenses that are priced (well) below the top end lenses, but that score very high on IQ.