The new version introduces a few commands: all can be used via console, some via RCON. All of them will need admin status.

ScriptCommand ItemAdmin - Opens the GUI for changing item settings - No RCON
ScriptCommand FoundationRadius <radius> - changes the minimum distance between foundations of non-allied tribes and players
ScriptCommand LoadItems - Reloads the item database
ScriptCommand LoadSettings - Reloads global settings (currently only FoundationRadius)


All settings are stored in multiple files inside the Saved/SaveGames directory as .sav files.

They are:
ArkCustomizerItems.sav - Database of item changes
ArkCustomizerSettings.sav - Database of global settings changes

These files can be copied to multiple installations or shared with other people. A tool for external editing might come too. And of course you can prepare you settings in singleplayer, upload them to your server and then use a command to load them into the running game.