Should you really use a press drill to ensure the neck holes are done 100% correctly?
Yes, but if that's not possible:
Fit the neck to the body, clamp it in place and fit the two E strings to make sure it's properly aligned.
Drill the neck holes using the body holes as a guide (measure the depth first!).
They may not end up 100% perfect, but close enough for rock'n'roll.
But I agree, if you can get Warmoth stuff all the important holes are already drilled, and everything will align just fine.