I’d like to have one SSID use my dns server and another SSID to use Cloudflare dns server (this having filtering) can this be done? If not can I suggest it for a future upgrade?
In my experience that information needs to be set from your DHCP server. You might have to accomplish this using VLANs. Have each SSID on a different VLAN with different DNS settings.
I’m sure Alta Labs would also prefer to point out that quite a bit of filtering can be done using their built in filter 
Yes I think personally if it were me, I’d do this more centrally vs at the AP level, and have different VLANs and have your gateway do the rest. It’s more scalable and probably a better solution anyways Like @rutman286 said