Nothing prevents a grant recipient in the framework of an FCT funded project or a research unit to enroll in master or doctoral programs or others. However, master and doctoral grants may not be awarded for R&D projects or institutions, as their duration would only by great coincidence cover the time needed to acquire these academic degrees and, besides, these grants serve different objectives.
However, a research grant recipient in an R&D institution or project is, of course, free to simultaneously follow a master or a doctoral program.