Where does it say it won't count, did I miss something?
"(Perry and Jackson will remain tied for the most Hot 100 toppers from any album regardless of the performance of any singles from Confection. Should any song released from Confection reach No. 1, it would count as a Hot 100 No. 1 from Confection and not Dream)."
TCC is TD + 3 Bonus tracks, not a separate EP like Cannibal or The Fame Monster.
Interestingly enough Gaga wanted hers to be counted as its own album but interscope latched on a re-release. Of course those singles also didn't count for the regular album. I have a feeling they stepped out of the guidelines or something I don't think they changed the rules specifically for her.