This is a big debate, and I've slowly formed an opinion on the matter.
In real auto racing, cheat like hell. It's part of the game, and it's half the challenge (and fun).
In autocross, where it's all amatures trying to be the best and tweaking a car and driving it, it ruins the fun. If you are showing up for the first time, run where you should! I would ignore truly insignificant things: a stock but knauberized Contour can run in GS - that's just too much nitpicking. But a real mod, like an intake, should bump you - even if it doesn't really matter. CF hood? SM. Just run there, and compare times against stock.
There are exceptions. If you're trying to build a car for a class - like I am - and you are having trouble making it legal, run anyway. BUT, only if it gives you no significant advantage, and you let competitors know. When my HVAC inlet leaked and flooded my pass. footwell, I had to remove some sound-deadening that got moldy. That's a bump to prepared or something, and there's no way to replace it that's not expensive and a huge PITA. Aside from these technicalities, just run stock. I want an accusump, which gives no performance benifit (for me - there are reasons it's not allowed), and would help me with oil starvation. But, that's something I can help, so even though it doesn't make me faster, I'm doing without.
