Since version 2.9, BizHawk now offers Ares64, a Nintendo 64 emulator core that runs on Linux. The multiworld installer and companion app should offer a Linux version, and the plugin (BizHawk external tool) doesn't seem to be working without modifications either. Maybe also look into offering a Debian package source for easy installs and updates.
Considering a Debian package or similar out of scope for now since BizHawk itself doesn't provide one yet. Current plan is to use the same install and update flows as on Windows.
Since version 2.9, BizHawk now offers Ares64, a Nintendo 64 emulator core that runs on Linux. The multiworld installer and companion app should offer a Linux version, and the plugin (BizHawk external tool) doesn't seem to be working without modifications either. Maybe also look into offering a Debian package source for easy installs and updates.