Door replacement question: Take hinges off the donor door or off the car body?

One of my prius got hit and ran earlier this month. Not a ton of damage but badly dented up the skins of both the drivers side doors but no structural damage beyond that. I would use a PDR service but the other driver scraped the paint down to bare metal so it will need paint work.

Got lucky and found a set of nice near complete set of used doors from a junker in my cars color ($260 for both). Fixed any minor scratches and then cut/polished. Will still need to swap over some of the internals but they are pretty much ready for install when the time comes.

Question:
Is it better to leave the hinge on the body and mount the door to it?
or
Remove the hinge from the body and use the one already on the door?

How do you assure alignment is correct once mounted?

The irony of this question is that the donor front drivers door has no hinges and the driver back door does. So I am going to have to use both methods either way.