Logic has its own bypass system, but it isn’t working very well - at least not with Juce based plugins. The idea is that logic creates fades by itself, but something is broken. I can recreate the issue with the JUCE demo plugin. On the other hand the apple AU examples work ok, so it might be something the JUCE AU wrapper does that confuses logic. I wrote about that here:
In any case Logic Pro does not support the AU bypass parameter property, which is a shame. Maybe it does for AUv3, but I haven’t tested that.
That is why I started doing my own bypass stuff in the first place. I just want to give my customers the option to automate bypass in Logic without audio issues, but now I guess I’m steering towards another half-working mess and inconsistent behaviour between hosts. That is why I wonder how other people are dealing with the situation.