That issue is already recognized and it was done in one of your very own other topics and we already have a bug ticket to fix that. You are mixing 3 different issues in 1 topic. I apologize for the confusion, but you can see exactly firsthand why it's a problem to mix multiple issues in 1 topic.
forge.joomlapolis.com/issues/8568
I do not have a workaround for you. The issue is more than just that message not displaying. The entire indicator status of the subscription in the Subscriptions tab for pending payments/renewals is just not good and needs fixed.
And just for clarification, if there are multiple payment baskets for the same member same subscription, does it matter which one we process as paid and which ones we delete?
No.