Keith,
My apologies. I have over-paraphrased what you said. I should have said something like "effects." I too tremble for those clever lens designers.
My understanding is that at any surface, the light is refracted and so light passing at an angle through a flat filter will be refracted both on entry and exit. We all remember the bent stick in water. The emergent ray is parallel to the incident ray but shifted slightly sideways and I understand that this moves the point of focus by about a third of the thickness of the filter, so a thicker filter would have a greater effect. If the filter is of high quality there should be no other visible effect.
When the filter is between lens and film, this might have a very small effect on critical focusing that might be significant in some circumstances, such as a close-up of a flat surface using a wide aperture. The effect would be more pronounced with wide-angle lenses.
If the camera is focused with the filter in place, all this will automatically be taken into account. I suspect that for general landscape shots, at the usual small apertures, any effect would be undetectable.
It might seem rather clumsy to focus, remove the lens, insert the filter and replace the lens, but it could be done. I've sometimes removed a lens when the camera was in an awkward place, to see the aperture markings.
For lenses on the outside of the lens, the current fashion seems to be to add grad filters, a polariser and a big stopper, which fills me with horror.