this is kindof a pain in the rear...now, just to be safe I absolutely HAVE to write protect my skyrimprefs.ini because that buggy launcher sometimes decides I suddenly need "Low" or "High" graphic settings (depends on the angle of the moon, if I've sacrificed a goat, or if Elvis has been spotted today).
For me using the skse_loader skips the Launcher, but only if I run it as Administrator. If I'm using the Launcher I have to write-protect my INIs, including the ones in %LocalAppData%\Skyrim, as it'll just indiscriminately enable mods I want to keep disabled. I could just move them, but when you're testing a large number of mods for compatibility, it's extremely annoying. I don't know why they included this. I can see doing it if you actually open "Data Files", but it does it when you start up the Launcher.