I’ve heard of people drilling shoes, e.g. for 4 bolt cleats etc, so I’m sure it’d be fine. Rather than filing a longer slot, I’d just drill the holes where I wanted the clear fixings to go.
If you can, and for possible re-sale purposes, I’d consider whether you can customise the cleats rather than the shoes. Obviously you might have to do this a couple times a year depending on your cleats’ longevity.