The two builds are made from the same source code and have 100% identical feature set.
I'm not expert in this and feel free to complete. The difference is in execution speed and memory management. This can make a difference with my other app
CSV Buddy that can read very large CSV files but with QAP it makes no real difference. The 64-bit should be a little bit faster but I never tested it.
So, in the end, it is your call. I distribute both for all my apps and let users choose.