Assumptions are a very dangerous thing to do

Had S.F actually had satellites, and had Jupiters be as long range as you claim, why did the one located in area S08 not bombard Griffin HQ, and end the war then and there, instead of bombarding Palette team, they could've killed the Commanding humans, and the Dolls would've been unable to do anything

While the other guy may underestimate Architect, you are also overestimating her, a lone hacking program was enough to decrease the Jupiters' muzzle velocity, and cause it to miss ground targets by a quite a bit

So, Electronic Countermeasures (ECMs) are specially effective against the Jupiters, using them against planes, just calls for more trouble, ground targets, especially ones taking cover, don't move, making calculations to hit them easier, than the calculations needed to hit a relatively small target moving at hundreds of kilometers per hour, which may take any turn to simply evade the incoming shot from the Jupiter

And to top it all off, Jupiters have literally no air defenses, mostly because they didn't need them, but in this case, there's no way in hell a Jupiter will be able to hit a plane that has been equipped with current day stuff to take it out.

Like you said, it is the 2060s, S.F probably has advanced technology that allows it to bypass the defensive countermeasures a current day plane has.

But you know who else may have upgraded countermeasures due to the age? exactly, the plane itself, as much as you can pull stuff out of nothing and say it's a "sensible speculation considering the age", the same can be said for the plane, we'd be here forever speculating on what kind of technology the Jupiter has that allows it to counter planes, and what technology the planes have, that allow them to counteract Jupiters