That question can only be meaningfully answered on a case by case basis. Many of them do cross the line as currently implemented in my opinion; to what extent varies. Oftentimes there is a perfectly reasonable explanation for their design rooted in history (ex being created prior to the internet or some other technology). On the whole most of them seem to work well enough.
I would note that the presence of one flawed system does not serve as justification for others to exist as well. The world is certainly imperfect, but that is not a valid argument against improving it.
> places a huge need on such intermediaries being present
I don't dispute this - what I take issue with is the inability to opt out.
> being a for-profit gate-keeper guarantees they will be perceived as abusing such a role
Regarding app stores, the manufacturers could have trivially set them up such that it wasn't possible to abuse them. Functioning examples of such systems already exist. They specifically chose not to do this, so I do not think it is unreasonable to assume the worst about their intentions.