Once they rust (where do you live, if they rust like that?) just use steel wool to remove the paint and rust for a ‘natural’ appearance ike a Cooperman. Shouldn’t hurt the playability of the whistle.
No reason you can’t use steel wool on the insides. I do it all the time to clean up rust spots, polish tarnish and remove the paint spatters routinely found inside painted barrrels like Sweetones, Waltons and Feadogs. Personally, I think polishing out a barrel makes the whistle sound a little sweeter.