It is an interesting relation, although difficult to establish, that seems to be emerging in some sites.
In Moreiros 2, several rocks with cup marks were identified the periphery of the enclosures.
Carved rocks with cup marks in the periphery of Moreiros 2 enclosure (images taken from Valera, Becker and Boaventura, (in press) "Moreiros 2 (Arronches, Portalegre). Geophysics and chronology of the internal enclosures"
At Torrão a rock also with cup marks is known near the enclosure and in Perdigões there is a rock inside the Chalcolithic enclosure, but outside of the Neolithic ones almost totally carved with cup marks, also present at one of the stones of the cromlech.
Carved rock with cup marks at Perdigões.
Of course we do not know the exact chronology of the cup marks, but in these three situations they are in the periphery of Late Neolithic ditched enclosures. What they mean we do not know. We can only speculate and many ideas were put forward. But maybe there is a relation between them and the practices that were taking place inside the enclosures.