Philosophically, I don’t think Popper was saying we should be intolerant to intolerance per se, but the fact that by doing so we end up in a conondrum of wheter we, as defenders of tolerance, are intolerant.

Sure, but he definitely concludes that intolerating intolerance is the way to go, despite the circular and self-referential nature of the issue. Like everything in life, there are exceptions that must be had to make things work, and tolerant people not tolerating intolerance is one of those necessary exceptions. There are plenty of really obvious things that humanity should not be tolerating, like rape, pedophilia, genocide, etc. If your argument is that just because you’re intolerant of racism, sexism, homophobia, etc, that means you’re a hypocrite and therefore no better than the racists, sexists, and homophobes themselves, that is a thoroughly invalid argument.