This seems like a very weird hill to die on, specifically concidering this is a feature I would want explicitly off and wouldn't care about existing.
It's editing 101, check your cuts are at a safe boundry of put in a fade. I've never seen an auto feature do what I want though and need to redo it anyway, so just doing nothing is half as much work.
I would much rather complain about lack of AAF support in logic but then again I would never recommend logic to anyone other than for music production work purely because that's the only use case the devs seem to care about.
You might be diligent to check your cuts in Sample Editor.
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.
I don't use logic. I find it to be no good but regardless I still wouldn't die on that hill.
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...
Unfortunately I am in position where I have to master mixes done in Logic and this backwards crap can easily add up to half an hour onto every track. Sick of it. Dying on that hill!
I mean put it in your requirements and reject the mix if it contains pops and clicks... Whoever did the mixing has the original with cuts so can add fades much much quicker than you can.
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.