Reboot patches are basically used for different things, but ultimately act the same. For the old3DS, they basically allow the signature patches from the CFW to exist when the system reboots to launch HMH games. This reboot is done to basically shutdown some the background functions like the web browser, so they can allocate more resources to the game. This is why games like Smash, MH, and Pokemon take so much longer to boot into the system, take forever to return to menu, and reboot when closing the system.
They also act as a way to reboot the system into the different mode, such as rebooting the system for TWL and AGB. Which also reboots the system when those are closed in order to return to the homemenu.
Basically they patches are used to patch those 3 different modes, survive booting into them, and survive booting out of them.
It will start, just GBA/DS(i) games won't work.