The best time to fit these monsters is before the car is painted.
Forget the factory holes.. weld 'em shut and start over, unless you're working with originals and you've been blessed with one of the cars like Scott mentions with perfect fitting mouldings.

Clamp them in place with "spring loaded hand clamps" & orient them for the best fit.

Drill & screw down one hole at a time using the same size pan head screw as your finish ones will be... no sense trashing your final attaching hardware.

Sometimes a slight reshaping of a fender line, etc. can be done for a minor misfit too.

This method also gives you time to send out your mouldings to be stripped & reanodized if you end up trashing the coating from manipulating them to fit. (Assuming they're anodized ones).
Cutting & rewelding them usually won't work... the different alloy of the filler rod will typically "take" the anodizing different and be visible.

And last... yes some fit better than others, but I haven't worked with enough different ones out there lately to comment on who's fit better than whose or who is selling who's parts. <-- sounds like a sentence from a Dr. Suess book... lol

Rick