The older marks are susceptible to a Meglithic Ruler; the younger ones aren't. Simple as that. Perhaps the crossover came with metal tools. Perhaps there were three main phases of carving. The last phase was more or less just scratches. The cupmarks in the roofstone of the Burren are markedly less eroded than their earthfast contemporaries.
The two sentences don't impinge upon each other at all. Currently the popular thinking is that bullauns are purely Celtic onwards. Some have been used in tombs and seem to be ignored: some saying they aren't bullauns but basins ... erm ... what's the difference folks?
There is a definite time gap in Ireland as far as evidence goes. All it needs is a continuity establishing. Associated C&Rs go some way to doing that.