So this is about sex in Macross??
It could have been easy for the Protoculture to make the Zentradi infertile in that they had the organs but not working.
The only reason I can think of for the Zentradi to be able to reproduce and also interbreed with humanity was because the Protoculture were expecting it to occur at some point, probably as part of their legacy if they went extinct.
After all at least a group of Protoculture programmed the ruins in Macross 7 to no be able to be access by humans nor Zentradi but only by the symbol of peace, Mylene a Zentradi-human hybrid.