In normal use, adapted EF lenses on the EOS R or RP should not suffer any major image-quality penalty just because of the sensor microlens design. Modern mirrorless lenses are generally designed to be fairly image-space telecentric, and a sensor that works well with them should also cope well with the more parallel ray paths from many EF lenses.

If there is any difference, it’s most likely to show up as a slight change in peripheral illumination toward the edges/corners rather than a broad loss of sharpness or overall quality. Whether that matters depends on your standards and the specific lens.

The greater risk, if any, would be with older or less telecentric lens designs rather than typical Canon EF lenses. So for a collection of EF lenses adapted to EOS R/RP, the practical answer is: generally no meaningful downside, with at most slight corner illumination differences in some cases.