It would be extremely worrisome that the court admitted sub-licensors to add something like the Commons Clause to software they get under the GPL-like licenses; it would completely invalidate them for all purposes, turning them into MIT-like permissive licenses instead.
I believe that similar reasoning would apply to the AGPL.
It’s generally not against trademark law to refer to a combination of things. I can say that I use Microsoft Windows + Adobe Photoshop, as long as I don’t claim that Photoshop is part of Microsoft Windows, no trademark confusion will result.
What might get you in trouble is to modify the Apache license text itself to add an additional clause in the middle somewhere, or to call that modified version it “Apache 2 licensed” without any qualification.
The argument that "Apache + Commons Clause" is a "combination" is straightforward to counter. The "Commons Clause" is not additive — it fundamentally changes the license, making it more restrictive and taking away potential uses. Consumers could not count on being able to do the things with software under such a license that they would ordinarily expect to be able to do with "Apache" licensed software, which damages the "Apache" brand.
In any case, it's not clear that it's worthwhile to go up against a sympathetic defendant like the ASF and make such an argument for limited benefit.
I was under the impression that it was Commons Clause that people started avoiding in favor of other "cloud protection licenses", both to avoid possible confusion and because Commons Clause got visceral reactions from some members of FLOSS community. Unfortunately, other similar licenses are less recognizable. The whole point of generic licenses is that they should be well known, widely used, and the legal departments already know their tradeoffs. If each company writes their own license then this makes it difficult for other companies to use their software, because legal departments need to check every license separately.
Is there a generic license that is the same (in spirit) as Apache + Commons Clause?
This has been always the point. All GPL licenses have a similar clause.