I just got mine about 3 weeks ago, so I haven’t had a chance to record with it. However, just monitoring it through speakers or headphones I do not hear any noise at all. This could depend on what types of modules you have installed though. I have mostly simple analog modules in my case.
One issue I can think of with flipping the case upside down to orient the 1U row at the bottom is the case’s handle. It would definitely be in the way unless you always have the case flat on a tabletop or maybe on a guitar stand. Luckily, it should be super-easy to remove the handle or replace it with a folding one. Also, you might not be able to use the angled feet that come attached with the case. This is all assuming that you just want to try mounting your modules upside-down. If you are thinking of modding the actual rails in the case, I have no idea. The people at Intellijel are super-responsive though, so I’d ask them.