The rootkit scan starts 8 minutes after boot (as far as I'm aware), so it shouldn't impact adversely during boot.
It is looking in areas where rootkits tend to hide or use to obfuscate them. If avast did detect a rootkit, then it would display an alert window to tell you so. It should (from memory) offer the user options in the alert window, not to delete, etc.
I think what you are seeing in the log file is more advisory, e.g. reporting a hidden registry entry, not necessarily that it has found a rootkit.