For what it's worth, the main argument against the ideas in the Eve Tek Tank thread was that they would be utterly game breaking or don't even really make practical sense w.r.t. how they could even fit into OP2 (either completely out of line with the canon of the story or don't even make sense in the game environment presented... for example, how would you even interact with a wormhole in game? Do vehicles drive through it, or do you get teleported to a different map, or what?). I think it's also fair to say that wormholes fall outside of hard sci-fi, we have no idea how to create them let alone whether they exist at all, or can even exist in the real universe... at least most of the ideas in OP2 are believable with modern tech, even if they took a bit of creative license with them.
As to your other gripes which strike me as somewhat of a strawman argument, not to mention, "how they work" are described in the game's help file along with some extra backstory, I would recommend reading the unit reference there:
-Boptronics = Inorganic circuits infused with organic components. Sure that works in Star Trek Voyager, or the Strogg in Quake or the Reapers in Mass Effect, but none of these attempt to justify how they work in reality. Even Outpost 2 doesn't explain how it works.
I think this was a product of the era OP2 was created in; biological computers have been a topic of research for a while now, especially around that time, and the idea seems feasible enough albeit impractical. I strongly think if OP2's story were re-written today, we would probably be discussing AI rather than computers with proteins in them; keep in mind that "everyday" AI and machine learning weren't practical in the 90s like it is today with the massively parallel programmable compute devices we have today (GPUs, matrix math ASICs, etc).
-Agridomes = Generates food out of thin air. Have to manage food for colonists, but not water consumption? And who have heard of a farm that can generate enough food for 40 people, requiring only 1 worker, and provide all the necessary caloric, protein, vitamin and mineral requirements for life?
This is obviously an abstraction for gameplay simplification. OP2 has enough micromanagement as-is, I think "food" can be simplified to mean food, water, environmental control, waste handling/reuse, etc. Same thing with the worker requirements for buildings, though it's mentioned throughout the story and help file that Agridomes are highly automated so it might be feasible to run the entire facility with one person. After all, this article claims that as of 2014, one farmer could feed 155 people:
https://www.thegazette.com/government-politics/fact-check-reynolds-says-one-iowa-farmer-feeds-155-people-worldwide/ (looking at other websites came up with similar figures, and for all we know this might be even higher in the OP2 world since a lot of that food isn't being produced to feed to animals/feedstock for ethanol production/etc as it is in the real world).
-Weaponized Lasers/Microwave = The power supply necessary to get these to work is insane, to bring them up to the point of melting tank armor. Also they are super finicky to being hit by projectiles (a cracked lens means your laser won't hit what you want it to), require constant cleaning of the lens, and are very prone to overheating.
Well, the story tells us that vehicles have onboard fusion reactors, so I would guess that would satisfy the power requirements. As to the rest, I think that the HP / damage abstraction that exists is sufficient for gameplay reasons (of course all weapons systems require regular maintenance; it wouldn't be very fun if you had to constantly bring your units back to a garage for repairs/lens cleaning/whatever other thing we don't care about for gameplay reasons). i.e. I suppose we could simulate everything down to the colonists doing laundry and using the toilet, but this is an RTS set on a Mars-like planet, not The Sims.
Further, masers (as I'd expect the microwave weapon and wireless power transmission described in-game to be using) likely wouldn't have an optical lens... probably some sort of waveguide/rectenna instead.
-Fusion Power = Technically the first Tokamak was built in the USSR in 1958. Since then many have built fusion reactors, and no one has managed to have a stable reaction with magnetic confinement. The most recent idea is inertial confinement, where hundreds of lasers hit some tritium to undergrow fusion. This still hasn't resulted in stable fusion. So, the developers of the game would have known this, after all the fusion reactor IS called a Tokamak in the game.
The wikipedia article for Tokamak suggests that there have been plenty of successful magnetic confinement fusion experiements, just none with a gain factor of more than 1 (i.e. they consume more power than they produce). I don't think it's a completely unfair assumption that in the OP2 near-future timeline, breakeven fusion might be a viable power source.
re: inertial vs magnetic confinement, keep in mind that large ICF facilities such as NIF didn't exist at the time OP2 was released, and it appears that most fusion experiments in the 90s involved tokamak-style designs, so that would probably explain why they went with the tokamak in OP2.