Rebuilding my rear wheel, the flange/spoke holes are slightly deformed from the previous build so do I reuse the same holes as before ie spokes inside/outside the wheels the same formation as before

OR use the alternate spoke holes so spokes are poulling against a non deformed section of the spoke hole/flange?

I was going to do the latter – use alternate config, but I put the first spoke in and it doesn't seat too well, will it 'pop' into place under tension or should I go back to original configuration?

Supposedly you should reuse existing notches…

I would always reuse the hub in the same way. They can creak if built the other way though I doubt it actually makes any functional difference.

I would reuse the rim in the same way as before too.