I'm going to answer this in reverse order of how you wrote it.
The Calderon family seems to be in the most hazard of any ruling clan in the Human Sphere. Yeah I know life is harsh in the Periphery but scions disappear or get killed a lot more than average. I would wager that the Centrellas and Avellars live without the fear of a sudden demise that the Calderons have.
Is it more hazardous for Calderons or did Thomas' kids just have worse luck?
Edward was killed in a dropship accident
Janice contracted Brisbane Virus
Ian left to join a merc unit
Felix "vanished" on a star mapping mission (but speculation is that he left the Concordat since he did not want to be Protector and disliked governing)
Jeffrey got screwed by the writers.
I don't think the Calderons live in fear of sudden demise or being targeted by assassins. Maybe the argument could be made that the Calderons spend less time in their palace and more time traveling among their people, exposing them to diseases or travel accidents.
Well what prompted this discussion is Bullrun Concepts (who fled the realm to make upgraded Locusts) and the Mosquito (as proposed by masterarminas) which are different pathways then canon. These optimization efforts do create a possibilities for change.
I will say that butterfly wings and unintended consequences play into my alternate setting a bunch. In other words everything Hanse does creates ripples that change events and characters for the better or worse. What doesn't change as rapidly is the location of a Star League Cache per say and if any significant find is in or near the Taurian Concordat that could be a source of conflict possibly.
In the Canon setting we already have great unrest in the TC from 3051-3055. Periphery 2e. p.1 on 3051 Marshal Doru was already calling out Thomas' policies as madness and "prompted widespread doubt among many who had once been the Protector's staunch supporters."
"Factions in Taurian society who had long since opposed the Protector looked to Marshal Doru as a potential savior" "assumed he would also willing replace Jeffrey Calderon should the heir-apparent prove to be a chip off the old block"
"Marshal Doru gained his greatest support among the Taurian Defence Force, many of whom had grown tired of the constant vigilance against a war that never came"
See also the sidebar on Page 12 about how the TDF was not able to chase pirates threatening the TC and how they were pissed at the Protector about his decision.
Handbook MPS adds more details about the Far Lookers efforts to undermine the Protector.
In 3053 Jeffrey Calderon was already working with Marshal Doru to restore sanity to the Concordat.
I agree there a ripple effects from events, but the biggest ripples happen the furthest away - for example in 3052 let's say Hanse starts planning to deal with WOB and the Jihad, or to counter the Trinity Alliance. in 3052 the Taurian situation is almost at its climax- all the pieces for Thomas being removed from office are already there. At most maybe this moves it up by a year, which means the Canopian Alliance is not fully worked out. The Concordat is at its boiling point, I just don't see much changing between 3052 and 3055- after that yeah a lot could change.
I like the third party angle but really see the Taurians as a third or fourth tier concern for Hanse himself.
Again if Hanse knows what is going to happen why not make a small effort that could pay off big time. If the TC and SIC develop close ties (even if the TC and FC don't) it makes it less likely that the TC would be willing to go to war against the SIC. (yes it could happen but it is less likely).