There totally ARE designs where you are trusting your GM to limit content that are not just fine, but good! SR has some! Fame, for example, is a quality banned at many a table just because it is very disruptive to the campaign's dynamic, but it exists because it allows very interesting stories to exist if the GM is cool with it. Fame earns its right to exist despite being something that many GMs won't allow at their table, because it serves a purpose. You don't need to contextualize taking fame as 'abusive' to ban it from your table, it can just not be a good fit. You can just say "nah" for Fame and it is totally clear both why you said it and why it is in the book despite the GM saying "nah."
I agree with the rest of your post, and wanted to add something, which is: I think moving ill-fitting rules to sourcebooks can help.
For example, hypothetically consider moving Fame out of the CRB and putting it in No Future, which contains other rules for PCs from sports, trid, or music backgrounds. I think this sends a strong implicit message that "this is not a quality that's going to play well in most Shadowrun campaigns, but if you're making stories a bit off the beaten track, here's a quality that can help you tell those stories." Same thing with, say, the DocWagon supplement, or the Lone Star one from the 2e days. These contain rules and ideas that aren't very useful to a "traditional" shadowrunner-focused campaign. but have their place for people who want to run those sorts of campaigns.
I think telling a player "no, we're generating shadowrunners, so you shouldn't take Fame" is a smoother conversation if Fame is in a sourcebook compared to if Fame is in the CRB. And then the CRB can remain focused and streamlined, as far as possible, by not trying to offer too many incompatible things.
Going back to the topic, I agree that (as I understand it from here -- I don't have the book) it's baffling that Impaired Attribute made it into SR6e at all. The argument that "GMs can just fix that" doesn't carry much water with me, especially as it's being deployed all over the place. Just how many things can a GM be reasonably expected to be fixing? I can't even carry in my head all the 5e things that concern me from a game balance perspective, let alone what to do about them.
Something I've found since reading a lot of stuff on here and r/shadowrun is a significant array of things in SR5 that can be game breaking if not handled well by the GM, but that I totally missed when I read the book. Consider Quickening. I missed this entirely, tucked away in the Magic chapter. But it's extremely common knowledge in discussion groups that quickening should either be banned, nerfed, or handled very carefully by the GM to emphasise its drawbacks. It's a little landmine, lurking the rules, waiting for my group to step on it, but I was blind to the danger. How many more landmines like that are there? How many GMs will overlook Impaired Attribute and start campaigns with 6e characters who abuse it for cheap munchkin trickery? How many novice GMs are there who can't spot this stuff and aren't active in discussion forums and so, in naivety, follow the rules and get the table into trouble?
I'd much rather the rules had no landmines in the first place.