If you dual-boot multiple Linux systems you can still administer any of the ones you're not currently running via chroot at any time, and that works fine whether you've got third-party repositories or not. A chroot is also what you'd use to reinstall the bootloader on a system where Windows has nuked the MBR or the EFI vars or whatever.

There might be some edge cases like software that requires a physical hardware token to be installed for licensing purposes is very aggressive, so it might also try to check if it's running in a chroot, container, or VM and refuse to play nice or something like that. But generally you can do basically anything in a chroot that you might do in a local container, and 99% of what you might do in a local VM.