The deal is that having 1 district type with 2 zones means that, unless you have full use to all its jobs, you are wasting your district investment and planet size by having undesired jobs instead of the desired ones, because you could've had 2 zones providing desired jobs instead. How is that a big deal? Take the most obvious example: CG, which normally come at expense of alloys for non-gestalt empires. The zones change impacts alloy/CG dynamic the heaviest, especially in early game (say, first 20-30 years, 3 planets). Zone mechanic impacts non-gestalts the most. Gestalt empires, on the other hand are much less impacted by zones, they have one less resource to manage.
In live, for example, the optimal player controls consumer goods through the time axis by playing with designations: stockpiling as much early on, and switching off CG production for a couple of decades later (usually, when they unlock megaforges), and/or playing with CG/alloy designations to have just enough CG, this allows a near perfect balance between alloys/cg, at expense of player attention: not playing attention will mean hitting a CG deficit situation. If you need your alloy planet on CG duty for, say 20-25% of the time, then you can have that exactly. This dynamic will be entirely gone.
The zone system heavily penalizes non-gestalt empires: in live you could just play with designations free of charge and trade alloy for cg production untaxed whenever you needed them. Now you'll have to play a zone mineral tax to switch one alloy zone to CG, and a further alloy and district tax, by losing away potential alloy jobs to excess cg jobs because the split is fixed 50/50 and is not granular. It's not a just matter of simply getting unwanted CG jobs, but that those jobs come at expense of alloy ones. Before, if you needed a planed on CG duty 25% of the time, you could have that. Now you lose 50% of district alloy jobs, and then get to priorize/depriorize the remaining 50% cg jobs as needed. Before a non-gestalt could have 75-80% of their alloy planet's alloy output by switching designations, now it will be a fixed 50%, is a 25-30% difference not a big deal?
Why not just have a separate, additional planet just for CG? This was not needed before, and will be necessary because losing 50% on the alloy planet is waay too much, but those will be additional costs in time and resources that a gestalt would not need to incur. A new planet costs resources, and what makes it valuable are the pops. Static pop growth per planet is gone, so a planet's inherent value is lessened. The colony ship, resettling pops and building urban districts cost resources, districts cost a lot of time too. Pops that are resettled to a CG planet are still pops that could've produced alloys, and each incurs an energy tax to resettle. And even then, again, a extra CG planet would still incur wasted pops and resources on excess CG, because fine-tuning would incur resettlement costs. And in the new system non-capital planets get only 1 zone slot until later tech, halving the value of their urban district, so you are even further penalized if you want a separate CG planet, for the first couple of decades, maybe even three if you're unlucky with tech rolls and don't get colonial centralization. Granular control of CG/Alloys dynamic is going to be much more expensive, and it's something that does not impact gestalts nearly as much.
If, instead:
a) each zone provided double jobs but district slots were spent on upgrading individual zones instead, maybe in some kind of point allocation system, where you could freely distribute the invested district development as the player wanted or,
b) there were two urban districts, with 1 zone each, and zones provided double jobs
A non-gestalt player could have, say 15 alloy districts and 3 cg ones on their capital. It would still be less player control than designations, but better than the what is currently intended to be.
