Can I just mix some of the same modified white thin-set to fill in a couple of small joints as grout
You could, I can't say I've never done it myself.
The problem will be the thinset will be much more sticky than grout would be and therefore harder to clean up. You will constantly be dragging the thinset out of the joint. Also thinset is likely to sag and not stay in a vertical joint. Just depends on how wide of a joint you are talking about.