Unfortunately I'm not on the SpamAssassin Bayes modules -- I wrote my own Bayes Engine because I wanted to do that and then thought about including the Rules results from SpamAssassin. I don't know where this might be going, but it seems to be working extremely well for me based on a training set of just a couple hundred emails in total.
Don't see this as a problem. Someone, I forget who, has a Bayes chained to an SA setup, I think the Bayes comes first, but I don't recall. He was claiming good results from chained classifiers using slightly different data and methods. This seems like a reasonably possible contention to me.
If you have a pre-existing Bayes mail filter, and it runs as a filter in a pipe or the like, then basically what you want to do seems very simple to me, at least conceptually. Just run the mail through SA first and then into your classifier. The rule names hit along with their scores will be in the header of the mail you process in your classifier, and thus, as long as you don't ignore header data, the rule names are there to process. No need even to modify SA. In fact you can get a header with just the rule names hit without the scores, so you don't have the score values being scored as tokens.
The only case where you would have to modify SA in I think either Check or PMS is if you really did want to bloat every mail with the names of all of the rules in the SA database, rather than just those pertanent to the mail at hand.
I hink the trick is simply looking at your mail chain and figuring out how to insert a call to SA before the call to your own Bayes module.
Loren