I was having same problem - to set custom order of attributes.
I am syncing data with external source over API. Fortunately for me, I was able to delete all attributes on products (not attributes themselves) and resync it again.
Order of attribute array as I filled product was also visible order in wp eshop detail page.

I haven't found any plugin or solution for ordering attributes list. It's designed to be reordered on product.

Hint: I had to delete attributes by setting it to empty array, and then update product with ordered attribute array (update was not enough).