Is it true that you should avoid adjusting the EQ & gain on profiles?
No, there's nothing inherently wrong with it. The reason some people elect to not use it as much is it functions more like a studio EQ. The further you change a parameter, the further you get from the original source tone since they aren't meant to emulate the controls on the front of your specific amp. If someone wants to stay more true to the tone they mic'd, they're less likely to change a whole lot.
That being said, it's not as if the controls are unusable. They can be useful, at the very least, for boosting or shaving certain frequencies, especially with a different set of pickups. I notice the controls work well with some profiles, not so well with others, so it's better to use your ears and rely on your own judgement.