I would try the Advanced Post Types Order it works perfectly for me. Turns our that it can handle sorting for product within multiple categories without messing all ordering see http://www.nsp-code.com/woocommerce-sort-products-which-belong-to-multiple-categories/
Definitely I’m interest too, sorting categories differently per post basis would be a cool and interesting to feature.
This is something I had looking for months now, sorting categories differently for every product would be great !!! Hopefully someone came across such thing.
