Now that Picker is working in MP, I want to change the setting under startup, but I can't change it in game, and I can't change it out of game. How do I change those settings on the server? Is it saved inside the zip file?

Also, I have been using Long Reach and Picker over rides the reach to 30 tiles, I didn't expect that.

Startup settings can only be changed before the world is loaded (at the new/load game screen) under options--> Mods.

Picker overrides all the longreach mods that change the prototype, mods that change the runtime character_reach_modifier are unaffected.

For a headless server The settings will probably have to be edited on mod-settings.json file but I have not tested with a headless server.

If I make the save in SP then put it on an MP server, will it take the startup settings from picker in SP?

I believe so but I can't answer with 100% certainty

So are those settings saved in the save file of the game on creation? Where are the other settings saved? The mod settings work well but it's confusing. I have similar questions about where the in game blue print library is saved.

I found the location of the settings! Simply replace mod-settings.json on the server with yours from the client and it works, it's in the root folder.

I would suggest putting a note in the description for others running it on a headless server.