Programming PIC 18F4550 using Bootloader
The setting of that configuration bit must match your hardware (when you use that pin of portb as GPIO, LVP must be off, when you want to program using LVp it must be on, and that pin must be low to run the application).

Thye settiing of that bit has nothing to do with the bootloader, but because the bootloader is the "application" that is programmed using the normal programming means, the LVP setting must be set in the bootloader.

Summary: the LVP setting must be present in the bootloader, but it is (in nearly all cases) totally independent of the bootloader, so you can change it to suit your needs.