Zoom hitting low sounds... ew. I just really don't like the sound of that. If she happens to be super jumping around keeping the head out of sight, you shouldn't need to worry about "is she going to go for a jump-in first or is she going to use the head that's out of my sight to hit me low first?"!
Honestly, zoom being low would be a great incentive to go Head-Off that fits in with Ms Fortune's mechanical theme, where Head-On is more solid and rounded, but Head-Off has monstrous pressure, mixup potential, and longer-range neutral, at the expense of when you fuck up your defensive options are RIP. It's not like Ms Fortune has any low-hitstop air normals so she couldn't get legitimate hard-to-blockables solo with her own head.
You can upback away from head attacks anyway, and in Beta you can upback away from air normals, so at neutral doing a jump in->Zoom or Jump-in->j.LK are both options that would be beaten by a pre-emptive upback if Ms Fortune was at normal jump height, and at neutral if she's doing sj->zoom then it really is your fault for not jumping earlier to escape zoom anyway.
The only situation of this being an actual real scary mixup is if you get a hard knockdown with head-off, then superjump on their wakeup, then meaty zoom will catch them upbacking, so they choose between block the zoom low(and risk you not doing zoom and coming down with a normal) or them upbacking and getting hit by zoom(which you might not be able to convert at superjump height?).
At normal height this would be much stronger, as meaty zoom or high or meaty zoom+block vs reversal would become really strong oki... But that seems like a pretty good incentive go to head-off, don't you think?
The entire problem prior to the mass of nerfs was that if you hit the head it wouldn't matter since it had barely any recovery, allowing her to potentially punish you or putting you into pressure for hitting the head WITH the head (!?!!?!??!) but now that it has more recovery, hitting the head locks it out like an assist. This makes improper head placement more punishing.
As the game gets more explored, people WILL find horrifying ways to punish Ms Fortune for existing. We already have terrifying vs solo fortune head punish combos that do ridiculous damage, so the obvious way to rek fortune is to snap her out to anchor which also renders her alpha counter very bad, then mix her up on incoming with an incoming mixup that hits the head first and is safe to her air super, so a launch->upback->call assist->something somthing something whatever.