I'd suggest the Dremel method, you'll get cleaner cuts by far. And I'm very familiar with cutting Lian Li cases, they are NOT easy to cut, they're harder than any other case I've ever cut, their alu is a much heavier guage. You're going to need A LOT of heavy duty cutting discs. Go SLOW and steady, the less you have to sand and grind to make it smooth the better and with that case it's gonna be difficult.
Do you plan on using any kind of trim or do you want to rivit the window in place? If you're trimming you can get away with a slightly sloppier cut but for riviting you want a very clean cut.
For cutting the plexi, same rules apply, go slow, but also take breaks in between because the tool will get hot and it'll gum up with the plexi, so stop every couple of inches, wait for things to cool down and start again. Patience is the most important thing.