Your concerns are three fold (technology, Ts, and the book defining ethics), so I'll go over my views in each field the same way.
With respect to biotech, specifically aging, yeah, you're right. Immortality is probably Bio 8 at most. If you want to patch it in, I'd recommend something like “if your calculated life expectancy is 500+, you are effectively immortal (barring accidents)” (tune the number as desired). At those levels, it makes very little balance difference (at good Cog and 500+ years you can quite a few professions at 10). I didn't bother changing it in my campaign because it makes little difference to society and no difference in the span of a single campaign. Generally, I figure any character who's going to live for another 100 years will live to see immortality invented, even in the base setting (Bio 11).
I've seen settings that go too far the other way. Orion's Arm comes to mind, with their appearant (from my perspective) insistence on solving all problems using biotech or hybridized biotech, regardless of relative costs. I figure that that setting's biotech simply outstripped its other technologies, so perhaps it really is cost and time effective to grow one's road networks there, rather that just have stone / rubber / plastic roads and microbots do continuous repairs on the off hours.
That said, I haven't seen any other setting, RPG or book, that has anything similar to metatech (I.e. hard science sociology and psychology), except Asmov's Foundation. And even Foundation didn't go to this level. It's far too easy to think of human advancement as purely scientific, and forget that the arts and society itself has been improving as well.
On the Ts… I disagree with your assessment. The Ts are certainly well meaning for humanity, but not for you, the inspectors. You are pawns of the Ts, and my players have the tendency to feel used after any session where my T has had a large part (although it rarely shows up in those sessions being the silent hand that puts the pieces into place and presses “play”). Inspectors die for the Patent Office. If my inspectors made a habit of requesting T intervention (especially direct intervention), they'd get their week's notice right fast. The Ts suffer from the strong observer effect, so direct intervention cripples them.
Also, the T's aren't omniscient. Differently-iscient certainly, but they only know the few fragments of the future that were important to send back. If a planet is at risk of being destroyed they might know a name and a date, and which inspectors to send. Nothing else. Because more information than that didn't change the outcome, so the bandwidth wasn't wasted on it.
On the book defining what is right and wrong in the rules? Yeah, it rubbed me the wrong way too a bit. There are only three places where I can see an issue though. The rule that walking into a replicator is death, the tendency to put the Union in a bad light, and the themes being stronger for baseline humans (this last one bothers me not at all).
The replicator = death is something I take a bit of issue with. Personally, if a non-replicant walked into a replicator, I'd ask for their character sheet. If a replicant wanted too, I'd charge their bank account for the cost of replication. I don't consider the replicant clones to be too bad for balance (not much worse than a group mind, except that the group mind doesn't want to lose any members). That said, I'd still ask the player to have the Plot Immunity “Send in the Clones” (or something similar), even if they don't have to spend twists on routine replication.
The Union's “slave matrix” thing I generally treat as a combination of utopia = distopia from outside, and general bigotry against the Union. We have a Union PC in our current campaign, and he deals with that bigotry all of the time (from the world and from the other PCs). The Union world of Sunset is almost a supporting character at this point, and has always been portrayed in a good light. If I'm trying to make them creepy, I do it by making the light they are portrayed in be almost too sterling perfect.
The more-themes-for-baseline-humans is something I see as simple game balance. Not from the “we want everyone to be on an even footing” perspective, but that we don't want the oldworlder to have to sit around in the truck all session because he can't go anywhere near a fight, communicate with anyone, or understand anything. I'd bore the player out of its mind. So… the plot favors him, even if his own skills don't.
The choice between high import for low capability characters and no balance there is a simple one. Do you want a simulation of a high tech environment, or a good story (in a high tech environment)? Draw the line where you will and adjust the rules to fit.
The few oldworlder NPCs I've had in campaign have been very minor characters, except Ezekiel the old worlder inspector. He mostly existed to show that a fresh, simple perspective can cut through all sorts of problems. That, and because having a farm with lots of dogs within sight of mile-high skyscrapers is just hilarious.
If there are any other cases of the rules dictating morality, I missed them.
So, yeah. You bring up good points. And yeah, editing the setting to your heart's content is probably the way to go for you. I've certainly done my fair share of editing.