I agree that this is a possibility, and careful consideration of the risks and benefits is required. px’s are probably a safe choice for most users: you could duplicate the native appearance down to the pixel, and all browsers support px’s.
I believe some people think: you adjust one variable, and now the whole entire app scales to the desired size… including margins, padding, and alignments.
Actually, if you’re worried about rem’s for whatever reason (difficulty in debugging, browser support, etc), you could just as easily modify the find/replace operation to keep everything in px.
Did I stop to think if I should? You bet. Would it work for you? Maybe – and it’s easy to try. Does it void your warranty? Very likely. Here be dragons (or raptors, as the case may be).