- You have to manually add mods to the game via downloading either individual mods, or from a zipfile.
- Although you can have multiple versions of the same mod in the game directory, it only picks the newest version and won't allow joining to a server with the older mod version that you do have installed.
- If you have more mods installed than the server has, you can't connect.
- You cannot join any vanilla servers if mods are present.
This program desperately needs a modpack manager that takes care of all these details automatically at pre-launch time, like Minecraft Feed The Beast / Curse / Twitch launcher, Minecraft AT Launcher, or Minecraft Technic Launcher.
And note of course that Mojang does not create any such launchers, so the Factorio staff do not need to be involved with such a project with this either, as all settings and directory locations are twiddled before the game proper even launches.