Again I could be wrong, but I think with the option to buy it's nearly always down to the club that have loaned the player whether it goes ahead. I think the fee get's agreed beforehand and then it's acts as a minimum fee realease clause (for that club only) until a certain expiry date passed. As I said that's purely an assumption, but it would seem odd to pay a loan fee of 2m to fix a future fee that can then be amended by the selling club. As you've said transfers are probably much more detailed/complicated than us fans realise and we're all kind of second guessing.
He's likely to miss the first 3 games accoring to Pardew so there's still 35 league games to go after that so hopefully he won't be missing too much of the league campaign. Having said that 99% of what comes out of Pardew's mouth is utter garbage so who knows