As far as I know you only have to do that if you will NOT be using the sensorless endstops. If you are are using the sensorless endstops, or no endstops at all, then you don’t need to modify anything.
I read somewhere if you configure your endstops for NO, you can also use them with sensorless homing or maybe as MAX stops maybe? This would be nice incase your machine decides it wants to yeet itself into +x/y/z (if you home to -x/y/z).
Why not? If you bend the pin and needed the pin later on, 99% of the time it will break when trying to bend it straight again. So there’s really no loss just cutting it off to start. Cutting also allows a better connection IMHO; bent pins prevent full insertion.
If you are a bit OCD like me, you might actually desolder the pins instead of cutting, so it’s easier to use the pin later on if needed. Desoldering a cutoff pin is a PITA in comparison to desoldering a full pin that you can grab and pull with pliers.
Edit: I am pretty sure the reason for the instructions recommending a bend, is it doesn’t require cutting tools to do. This project is intended for novices who may not have flush cutters on hand.