Autobuilds are "beta" builds, like stable release builds but with all the latest changes from git.
They're the easy way to play or host the latest development version. Like stable releases they include source code and an easy way to compile it for various CPUs.
If you "installed" Xonotic by unpacking the stable release zip you can update it to the latest autobuild using the scripts located in misc/tools/rsync-updater (use update-to-autobuild.bat if you're on Windows, update-to-autobuild.sh on Linux and Mac). You can also download an autobuild zip.
It's best to make a copy of the original Xonotic directory first in case you wanna go back to using the release but you can also go back by using the update-to-release scripts. Releases and autobuilds should be able to coexist (they will share the same config though, unless you use something like -userdir).
Autobuilds (and git builds) are compatible with the same servers as the latest release. When you connect to a server, Xonotic downloads the gamelogic from it (and runs it sandboxed) so you always use the same version as the server. Autobuilds therefore "only" affect the gamelogic of local or hosted games, the engine (rendering, input, ...), assets (models, sounds, ...), menu, config and scripts.