As far as I know, we haven´t yet found a way to skip those coins, since it´s still allowed to collect them in a Low% run, which you can see in the Category Extensions (as long as you lose them in a ghost battle afterwards).

However, Banananana, our main glitch hunter, has been theorizing about using OoB in Clockworks with the help of a spool, which you can find in the Warehouse. (Or with a bomb in Finishing Room, but that probably wouldn´t help skipping these pesky coins.) But I don´t know how testing this went. It´s worth mentioning that Purple Toad Skip in E-2 has been discovered this January, the first ever viable OoB route in Dark Moon Speedrunning History, so OoB might hold a lot for the future. But Banananana should probably give his final input here.