Why doesn’t Proton strongly encourage paying anonymously like some services and do they log more data than others? Is this concerning for you?

I think you are conflating privacy with anonymity.

Proton was founded and continues to be a privacy focused company. It is possible to use their services anonymously but that is not their focus.

In general, being actually anonymous is extremely difficult and easily compromised by any slight mistake. Going through the effort of paying for proton mail anonymously is likely not worth the effort for 99% of users as something else they are doing or failing to do will eventually compromise their identity anyway.