In these cases, the ship OL has locked *is not the ship modifying the dice*. OL is. In just the same way he is when he uses Juke despite the fact that it's his target's dice he's changing. OL does not block them because he does not block *himself* from modifying dice.
It doesn't matter which ship owns the relevant upgrade. It doesn't matter which step it takes place in. It doesn't matter which ship's dice are being modified. It matters which ship is doing the modifying. If it's the locked ship, the mod fails. If it's anyone else (Omega Leader, OGP with Palpatine on board, some putative other upgrade) the mod succeeds.
As currently written anyway; this could all change with an FAQ or with errata to those cards, but I doubt it would.