The "Button" is left of the Goto Zero button. It calls the M31 macro. I'm not sure how that macro works, as I use my own macro.
The only way to modify machine coordinates is to home the machine. If you have no home switches, the machine basically homes "in place".
Yes, you have to click Reset whenever a limit switch is hit. Non negotiiable.
You can always add any LED's you want to the run screen.
Not sure what you mean by "discreet message options". There are a variety of built in messages, and you can't change or edit them. But you can add your own via macros.
The Apply button is now redundant in the latest versions, and you no longer need to use it. The Save button does both Apply and Save. Apply was required in earlier versions, but no longer.
Yes, find the Profiles tab, and you can create as many profiles as you like. The easiest way to use them is with a shortcut with a command line switch to start the specific profiles. I'd highly recommend not using the default profile, as it always get's updated with UCCNC updates, which can cause you to lose any changes you might make. Custom profiles are not affected by updates, with the exception of the UCCNC.exe file.