Jumper on the board just affects if the contents of the ROM are copied to fast ram or not. No software is needed for that and it's purely for the speed. It's faster to read from fast ram than from rom.
Blizkick is made to modify the rom stored in the fast ram. You can replace the current rom with completely different version and/or apply different patches to rom. Blizkick comes with bunch of useful patches itself, but you also can add other patches to it. For example you can separate rom updates from OS3.5/3.9 setpatch and apply them with Blizkick instead (then you can avoid one extra reboot by setpatch, when you have two reboot on cold boot in worst case). So, because Blizkick uses rom stored in fastmem, you need maprom option enabled to be able use it.
No chipram is harmed in either cases in practise. 0,5M of fastram is used when maprom is enabled.