Only 9 Channels are set with the Rules but Workspace shows 13 Channels
The dimension that is set as a Channel Detail dimension does not look to be Referring Domain as the latter does not return "www." prefix. So it looks to be a custom variable, it's not clear how it's set.
The second criteria in SEO rule is not needed. I wonder how the Paid Search rule is set, maybe it's configured incorrectly and paid search is not getting intercepted before the Referral rule.
There are too many uncertainty in the shared input. I would advise to reread the documentation and then review not only the marketing channels, but also Paid Search detection rules.
Regarding the last questions, add the payment gates to internal filters to avoid conversion allocation to referrals.