The best would be to ask a Gentoo user. :D

Disadvantage (besides the update procedure mentioned by the other answers here) is, it might take lot of time, download lot of dependencies and files and need additional space on your drive to compile. It can be a hassle to install and setup the required tools and libraries too. This highly depends on the project itself if its worth it. In example nobody in their right mind wants to compile their web browser (Firefox, Chromium, whatever) themselves (sorry if I offended someone with that. :D). But a simple and short C program is as simple as running make command in example (given the dependencies are installed, which are most likely for simple programs after a few programs have been compiled).

Most of the time you don't need to compile software. Especially if you trust the source or its in the official repositories of your distribution.

Can it mess with my system in any way?

Depends on what you mean by that.