Proposition, remove SACU upgrades entirely, instead have a selection of uniquely balanced units for different intended roles.
The main reasoning for doing so is simple, it would significantly boost freedom to tweak and balance each type of SACU. For example, instead of having to give every SACU the same base movement speed and the same upgrade giving the same regen boost, one could easily choose rambos to move slower but have even higher regen, support units to move faster but have slightly lower regen, or any veriation their of.
As a secondary benfit, it also streamlines and standardizes the process of picking and building units, making it fit the already well established methodology used in all other factories.
Besides, there is never any good reason to go and get, for example, a ras preset and resign all the upgrades into a rambo. Just go and build another rambo, it would be faster, cheaper and easier.

Ok thats the big thing out of the way, now for smaller balance details.

UEF engineering upgrade is largely redundant. If you need lots of build power over long range, build kennels. If you need the ability to start building t3 buildings anywhere on the map, just use a transport to move t3 engies or the SACU its self. If you do want to have the SACU to have engie drones, then at least cut it down to one upgrade teir instead of two.
I am all in favor of faction diversity, but in this exact case functionality has been sacrifeced to for the cause.

The base stats of unupgraded SACUs are absurdly high. This was fine before, but now with the intention of lowering them down to fit in with t3 land, being able to build a non experimental unit with a hp over 15k and high regen ontop is excessive. Additionally, the fact that only Aeon SACUs can be one hit killed by overcharge is a bit unfair. Lower the hitpoints of all factions unupgraded SACU to 15k or less.

Remove Aeon sacrifice upgrade and instead give it as an addition to the engie upgrade for no extra cost. Sacrifice is simply way to neiche to justify its existance as a seperate upgrade, ontop of being largely redundant (Two mutually exclusive construction upgrades, just why?)

Buff or replace seraphim SACU TML upgrade. Getting SACUs into play happens much later then getting T2 TML laucnher meaning its much eaiser to counter SACU missiles, they also cost significantly more to build and are semi redundant because you can just use the SACU to build TML laucnhers anyway. As it stands they have very little reason to use instead of other options.
I prepose a few possible changes:
Massively boost the range of the SACU TML so that it substantually out ranges T2 TML.
Buff stats of the TML projectile to differenciate from the t2 version (More missile hp, faster travel speed, larger AoE, EMP effect, stuff like that)
Replace the ability to build TMLs with a MML weapon, kind of like a land equivilent of the seraphim crusier.

Although you are right that the numbers dont line up, there is a significant detial you have missed, spesifically the fact that UEF nano regen ocupies the same slot as the engineering upgrades while the seraphim one doesnt. That is part of its 'cost' that you have to later replace it.

The perpose of the UEF nano is to be an early game boost to combat effectiveness, at the expense of being unviable in the late game, because of this it is cheap and does not allow the constructuon of t2 buildings.

The seraphim nano is the exact oposite, its intended as a more late game boost to surviveability without sacrificeing early game capacity.

Atlantis, a shallow (pun not intended) attempt at faction diversity. Of could have just been given a t3 carrier like everyone else but instead they got a t4 just to be different. But then it would be too different, so instead they got a t3.5

That roughly sums up the whole problem, the Atlantis doesn't know what it wants to be, a t3 aircraft carrier or a t4 submarine, so it tries and fails to be both at once.
It's not a good carrier because its mass cost per BP is over twice as much as other carriers, in fact it's literally cheaper to build a t3 air HQ from scratch if you want t3 air units.
It's not a good submarine because its massive size, slow speed and relatively low hp make it a pitifully easy target to destroy.

The only thing going for it are its relatively cheep cost for a t4 unit, and its decently powerful weapons.
Essentially it is a glass cannon, a quick to build but short term boost to firepower. A gimped monkey lord.

There are a few options on how to rectify this:
Take a heavier focus on the submarine aspect, make it a little smaller, boost its speed, add some anti torpedoes. Make it threatening to enemies naval units.
Take a heavier focus on its carrier aspect, give it much more build power, more powerful AA, maybe even Airstaging (if adding that to a submersible unit doesn't break everything).
Turn it into a dedicated support unit, a t4 cruiser wannabe, using its AA and torps to discourage incoming attacks to your navy while offering extensive sensor range and fighter support.

Jamming could be put into UEF SACUS at base (cant waste a slot if it doesnt take a slot!) but that does leave a gap in the support for preset and I can't think of anything useful to add there that isnt just a basic stat up like extra sensor range. I suppose there could be a 'high intensity jamming' upgrade that just amps the jamming effect up to 11.