I don't know anything about electric guitar but maybe the tuner cacated? Try with another one and see? Maybe can plug the guitar into the comp and use a software one. Just throwing out ideas here.

Or maybe the string old already like acoustic. My old acoustic sounded like out of tune even in tune because the strings were 3 years old, hehe.

Hmmm I find it best to tune my guitar even after the tech is done with it. Ear compared with electronics? Give me technology .

New strings somemore. Are they the same brand of strings you used before? But I don't think that will make the guitar sound out of tune.

I think best try another tuner. Strange. When you fret the string at the 12th fret, does the tuner say the string is in tune? Unlikely but maybe the tech screwed up the intonation.

That means intonation is good . Maybe people's ears something wrong xD.