Summary: even in BiS, mastery is probably better than haste with real fight conditions and the RNG involved in RPPM mechanics. However, a ratio of haste to mastery is optimal on average for patchwerk fights. This is probably what ShC is trying to get you to do but you can't just press auto-reforge to get there because ep is not automatically adjusted. The difference is likely ~1% no matter how you reforge though.
There's an option to force mastery > haste in ShC now. Check the Advanced tab (and make sure you adjust expertise appropriately as well, otherwise it will default to .7 and uncap you). This is what I use.