Along with the f parameter when it was introduced the canonical URL is something that should of been thought of beforehand. Since the f parameter has never been implemented on my site it's non issue for me. The introduction of the f parameter basically doubled the duplicate content on a site. This is something that should of at least been an option when introduced, I don't know if it's used for anything else now but when introduced it was only used to generate the who is online information for specific forums. The introduction of the canonical URL is telling a bot most of the links generated by phpBB are not the base URL ....
I dont' know what the consequences would be changing it now.... What i do know is despite the fact you have told Google the canonical URL does not include the fa parameter this and other topics on phpBB.com that are indexed contain it. It's ignoring it...