I'm certain you're very much aware of the difference in context between the two circumstances. In this particular case (for reasons I went into at length in a thread a while back I can't reasonably expect people to know existed), there are enough interactions in the air game that it's entirely possible to create a situation where there isn't a fix handy in every player's toolbox. The way thrust in engagement rolls and even initiative on the radar map means that a deliberately built unit can make itself functionally immortal in the skies with no counter.
That's a problem I (unsuccessfully) argued against from another time, but in this case since the Inability to effectively deal with a target also includes perfect protection for a C3 unit I think it's a little more important to fix.
What interactions would those be? If you want to shoot down something in the air something like
this is pretty inexpensive, and it moves 2 zones, so the Zugvogel isn't going to get away from it.
You mentioned custom units? Well that's always problematic, but that's not in standard rules, so it can be ignored.
How about you ECM the unit on the ground? you've only got to be 12" away from it, so if you have ECM, your opponent isn't going to get better than medium range out of their C3 anyway.
Putting a C3 "Server" on an aerospace is a far cry from "perfect" protection, and saying that "initiative" makes a C3 Server effectively immortal just because it's aerospace is a pretty weak reason to nerf something that exists in the fluff of the referenced unit (Yes, I know fluff aren't rules, but why make an errata just to contradict the fluff?).
The issue is that it's not supposed to be possible.
The answer "just kill the master" isn't really a valid answer when all the other roles for obstruction go out the window based on the platform.
ECM the "Client"
To illustrate the issue, I would be interested in hearing how you would approach neutralizing a C3M on a fighter with thrust 12a that doesn't want to engage.
We can figure out the average number of turns required to successfully do that for a number of different methods. It's really a subject I enjoy exploring, especially for aero units.
No such unit exists, so you're bringing customs into a standard rules argument. Beyond that,
ECM THE CLIENT UNIT.