Hey, I might do that! I would be worried about how that might affect the tone of the A string though... Try and see I suppose.
I was raising a saddle on a Quan Badass bridge and one of the set screws came out the bottom of the saddle. It launched across the room and took some great effort to find it. I have noticed that some bridges are designed for low action and if the saddles are raised too high it causes stress to the intonation screw. I have two basses with Kickass bridges and one has an aluminum shim under it so the saddles don't sit up too high. I have two G&L tributes and one SBMM that have a shim between the top of the bridge plate and under the saddles. It's just something I do because i'm weird. LOL!
Yes, I might file the sharp edges. But lower saddle + shim is also not a bad idea. Can I ask why you shim your basses? What purpose does that serve?