Above answer is correct. If you change inis you MUST shut down the server and overwrite the inis while the server is not running, otherweise your changes will have no effect.
Some additions:
Most of ServerDog's commands are inside UTeamFix too. ServerDog was meant as a "generic" administration tool to work with all mods (or most) but UTeamFix can take care of itself. You may still find ServerDog's UDP Query or the Informercials useful though.
Advanced options:
It's not possible to access the advanced options on the away server through unreal. If you have no access to the remote desktop, you will either need the commands (but not EVERY little setting may be settable) or you simply set up a duplicate of the away server on your home machine. There, just set up your home machine as the server you would want it on the away server. After all, you have full access on your home machine

When you're done setting everything up at home, shut down your server and copy the generated inis over to your away server.
Make sure both machines have all needed files, and remove any possible "version-conflict-prone" files on your home machine again when you're done.
In theory, everything is settable with commands, but that would require you to type a lot, use the exact class and variable names each time.... painful idea. I am aware some things are not settable via commands, but with every UTeamFix release more commands entered the patch, so should there ever come another, expect more commands to set stuff. I was also considering including an in-game menu but I was more focused on fixing stuff rather than adding comfort.