First of all, your understanding of 54(3) EPC seems to be right. More information can be found in the guidelines for examination where one can also read that the EP application has to be valid (e.g. not withdrawn) at the date of publication to qualify as prior art for 54(3).
Could the EP application be allowed to grant if the PCT application has not yet entered the European phase (i.e. is currently not a 54(3) document but could become one in the future), but would appear to be novelty destroying?
This, therefore, seems to be a correct interpretation. In theory. In practice, (almost) no european patent application will make it to a grant in less than 31 months. And if the examiner knew about an unpublished application (afaik they can search at least unpublished european apps and I think PCT too - plus the PCT will get published prior to the 31 months so they can find it then even if not), they'd simply wait.
Assuming however, some prior art did turn up after the grant - the course of action would be the same as for other prior art found after grant - do nothing. Know that the patent could be challenged and include that in a possible litigation strategy, other than that, you have a valid patent unless proven otherwise.
All in all, examiners never find all prior art, so the few cases where this particular possibility for hidden prior art might be the reason, there's really no important difference to cases with any other reason.