Lethal Company's mods are Thunderstore packages on BepInEx. Mortar installs BepInEx, searches Thunderstore alongside Nexus Mods, CurseForge and GitHub, and Add installs a package with its dependencies. A dependency still missing is flagged on the Load order tab and in Before you play.

Thunderstore links: ror2mm:// links (Install with Mod Manager) stay with your other manager until you turn on Handle Thunderstore links in Settings › Downloads (turn it off to hand them back). A link names no game, so it installs into the open game when that game has a Thunderstore community.
CurseForge links: turn on Handle CurseForge links in Settings › Downloads, or tick Open CurseForge Install links with Mortar on the Windows installer's last page. A mod for a managed game asks which profile it goes into; other games' links go back to the CurseForge app.
Vintage Story Mod DB links: turn on Handle Vintage Story Mod DB links in Settings › Downloads.
Play: BepInEx reads only the game's folder, so on each launch Mortar places the profile's BepInEx files beside the game (winhttp.dll, doorstop_config.ini) and removes them when the game exits (a crash is cleaned up at the next start). Plugins and settings stay in the profile; the log is BepInEx/LogOutput.log, also shown in the Console tab.
Launch options: profile menu › Edit profile, BepInEx group: Show the console window and Log level, applied at the next start.