Does disabling crops increase the chances of mutations while crossbreeding, or will they simply not spawn?
It just removes them from the choices for crossbreeding, and if I understand the random weighting correctly, that will also slightly reduce the chance of getting a mutation. I can see how one might think "oh, I'll plant some instances of the parent crop, then disable it so I only get mutations from the crossbreeding spots", but I tried that in a test world, and the parent crops weren't just invisible, the crop sticks went empty (I could tell because they were still empty after I re-enabled the parent crop).
Edit: on the other hand, until https://bt.industrial-craft.net/view.php?id=2593 is fixed, I'm not sure how much it would help to be able to tweak the chances of mutations anyway.
Something else I noticed: rose and reed do not have seeds listed in JEI, even though I have not disabled them via config.