@Tentha You'd still need to have a batch file with the content I posted, but it will keep plutonium updated and, as you said, it won't replace the custom images unless theres an update.
So basically adding the .exe to Plutonium\bin and changing the .bat content to
set plutopath=%localappdata%\Plutonium\
%plutopath%bin\plutonium-updater.exe -l -d %plutopath%
start "" "%plutopath%bin\plutonium-launcher-win32.exe"