However when you zoom in in the Arrange the way the waveform is rendered it seems like you are cutting on a zero crossing when in fact you are not.
It lies to you and leads you to believe you've done the right thing.
I have had the pleasure of working on tracks with dozens of clicks that I had to remove thanks to the laziness of Logic developers, pardon me for dying on the hill and spoiling your view.
There's many things I disliked about logic when I tried it and that led to my opinion on its only useful for music production, I would probably not even say editing...
More on the composition level. If I'm tracking it's into Pro Tools, any edits happen there too. I personally don't move out but other's do really prefer to do more production work in Logic so I would happily bounce out tracks for them. Ironically AAF would solve that problem too...
Regarding cuts on zero... I basically never do so all my cuts will have a crossfade, generally the real world is just a little too chaotic to have a zero crossing just about where I would prefer the cut...
And if they don't well, more work for them.
Or just add it to the bill, if you are clear upfront that it will add $$$ there's no issues there.
I've had sessions rejected by mastering engineers for stuff that I've had to correct, why make this your problem.