RE: Drilling a prop
If your press has a way to lock the vice down, then index the work with a bit that fits the existing hole. Secure the vice in position with the indexing drill bit chucked tightly and extended into the existing hole. Raise the bit and swap it out for the size hole you want and go for it.
If your props won't square up in the vice, that pretty much invalidates whatever accuracy special bits or indexing technique can provide. You really don't want to try to work the prop hubs to make them more square. You'd weaken the hubs. And APC hubs aren't what you'd call accurate castings. Sloped sides don't stay flat when the vice jaws close down on them.
APC's really aren't going to work well with precision setups. A hand reamer at least will follow the axis of the original hole. They do that accurately too.