skipBars is introduced in the Learning Manual (3.4.5 Scores and parts)
as a way of condensing multi-measure rests. Its only references in the
Manuals are regarding this function. I suspect its impact on notes
crossing barlines is either unintended or at least not thought through
I can't imagine a situation where the current behaviour would be
desirable (silently hiding a barline thus changing the length of a bar)
and it would certainly seem to be a very different use case than
condensing multi-measure rests.
I think the default behaviour (without touching skipBars) is ok, and agree that there's no apparent need for it to affect notes (the possible scenario with long notes and short empty bars seems implausible). So perhaps skipBars could be changed to only affect rests, or at the very least a different context property could be used as an example in the learning manual (or both).
I verified that \compressFullBarRests does indeed affect notes as well, so if you want to file a bug report then perhaps proceed on that basis.