Hi,
1. I was not able to reproduce the problem. The wholesale payment method, when selected is properly taken into account in the order. I invite you to check the orders I created on your website, which contain the payment methods, with the correct payment fees and the correct payment methods selected as a wholesaler.
2. For the orders "payment methods" filtering on the orders listing, the issue is that the filtering is done at the plugin level, not at the payment method level. So regardless which payment method you select, as long as it is the same payment plugin, you'll see all the orders of the payment plugin selected. We'll change that for next version for better consistency.