Any tuning system for guitar is going to be a compromise due to the change in string tension while fretting. The tidy geometric formulae don't take this into account when determining fret locations. So instead of equal-tempered, we need to tweak things a bit, and settle for well tempered tuning.

Having said that, if your tech adjusted the nut location, and I assume the bridge saddles as well, it should be easy to tweak the tuning a bit to arrive at an acceptable compromise. Chords should have just a hint of warble to them. It's like the way a human voice sounds a bit richer if there's a bit of tremolo in it. But anything beyond a subtle colouration indicates that is still not right.

Don't settle for less than pleasing results. I hear all manner of horror stories about the uneven Quality Control exercised at the Gibson factory. Have it examined very closely by someone who knows the ES-335 intimately. It may be that the bridge is in the wrong place, or something equally annoying.