Portal room (more importantly, end portal blocks) can get overridden by other structures such as mineshafts, ancient cities, and also the new trial chambers.

Step to Reproduce:
Load up a world with the seed given and go to the coordinates.

Trial Chambers Overrides Stronghold:
Seed: 940028760242419482
Coordinates: 1443 -17 -1505

Ancient City Overrides Stronghold:
Seed: -3307142256062781398
Coordinates: 786 -44 809

Expected Result:
Stronghold would replace the structure, rather than the structure replacing the stronghold

Observed Result:
The stronghold (and the end portal blocks) get replaced by said structure and you can't enter the end.