Love tres leches. I’ve made a small tres leches in a 5” cake pan, a small (6-7”) bundt, and mini bundtlets, so yes to cupcakes!
I do think you need to think ahead to serving as the cake will be soaked and soft, and you don’t want to be digging it out of a cupcake mold at that point (unless you’re using individual silicone molds that can be easily inverted).
(My last few rounds of tres leches were indianized like this.)