The two types of scan really have different functions, or rather, reasons for their use.
My understanding - and I'm not an expert - is that some malware resists deletion/termination when loaded, that is, when the OS is up and running.
In these cases often an application may be able to detect but not clean it. (Some security applications, eg: MBAM, offer to delete such malware on the next reboot.)
And Avast's boot time scan is precisely for that type of event.
In my experience, it takes a little longer than the normal scan, but I haven't timed it: that's just my impression.
Normally, a standard or thorough scan is adequate. The thorough scan will take longer, and is for situations where you suspect there may be malware on the computer.
The boot time scan is a follow-up, if malware was detected, and you want to be sure nothing remains, or it wasn't able to be cleaned during the normal scan.
