You can countersink it with some countersink bits that would be used on wood, but the ones designed for metal do work better. Don't countersink the holes since the bolt will align to the hole if it's countersunk, so you have no room for adjustment which is important to get the spindle aligned properly (i.e. in tram). If you need the head of the bolt below the surface of the aluminium, then counterbore the holes and use socket cap head bolts.

Other option is to make a 100mm wide spindle mount. If you can bolt it from the back then it shouldn't be too difficult. I've made one that's 110mm wide.