Yes, 55 days of antiviral therapy could definitely impact your time to seroconversion. What you are doing by taking antiviral therapy is preventing or reducing viral replication. If that is successful, less virus is “visible” to the immune system to make a response. If there is less or no virus to see, the immune system doesn’t know it needs to mount a response. That is a very lay explanation, but does that make sense to you?
I don’t agree with your assessment of the red spots in the urethra being somehow a placeholder against lesions on the shaft of the penis. Most men get herpes with an exposure to the urethra as well as the shaft of the penis and they still get penile lesions.
If you want a reliable antibody test, you will need to consider your use of antivirals as a potential problem.
Terri