First, I never heard of drilling holes into the tile through the toilet base holes.
You should have a toilet colar that fits directly over the drain hole. This colar is fastened to the floor and to the drain. On it you will have tracks all around the hole that you fit bolts into and they stick up in the air.
You then lift the base of the toilet and place and line up the holes with the protruding bolts and then slide it down on the colar. Then you screw down the nuts carefully and in stages to seat the base on the bolts.
Any other way like drilling holes is beyond me.
Sorry if I offended you or misunderstood your post.