I’ve baked pies where the filling prior to baking is very fluid (e.g. custard). To prevent a soggy crust, I’ll brush the bottom and sides of the unbaked pie crust with egg white and then bake it blind at ~200°C for 12-15 minutes. If that barrier can endure a liquid filling for another half an hour while baking, then I gotta believe that same film applied to the interior of a cookie dough cup will be able to handle milk for the 2-3 minutes it continues to exist at room temperature (seriously, those things look delicious).
That said, I’m with GilbertWham— just apply some reliably hydrophobic (and reliably sumptous) melted chocolate. I’d probably eat that in ninety seconds.
