If you include the SSID as a specific TLV attribute, then you can use that as a conditional in your access rule. But it shouldn't matter, as all the other RADIUS clients, if they do not understand the specially formatted Filter-ID that the EWC understands, then they should ignore it, and it won't affect anything else.
Specifically creating rules to only send the filter-ID back for that SSID becomes more complicated, unless you are using different policies for the same user on different SSIDs that are dynamically assigned, in which case you will need to more granularly write your access rules in NPS.