My guesses for why he's in the vault temporarily would be:
1. Logistics. From pics it looks like burial in that chapel requires the floor to be taken up and the coffins lowered in. It might be easier to only do that once.
2. Related to logistics: While the Queen is alive, there remains the chance that she could change her mind. She could decide that she wants her own tomb or whatever and it would be easier to move him from the vault than from underneath that chapel floor, if that became the case.
3. Family issues: He isn't related to any of the people in that chapel. Putting him in with his in-laws, but without the Queen, might be considered odd or something he didn't want.
Dunno. Those are just my guesses.