Yes, linking to Adwaita is a decision to use Adwaita theme by default, because the widgets in it are intentionally designed to work well with only with those specific colors, spacings, fonts, etc. But the app developer can override that afterwards if they have additional CSS.
>every distribution shipping GNOME is forced to consent to having Adwaita as the theme
Can you show where this quote came from? This makes no sense and I do not understand why someone would say this at all, any distribution shipping GNOME is free to modify the Adwaita theme or ship another theme, as Ubuntu is already doing for some time. GNOME developers may grumble about it and write more letters like this but they cannot stop them from doing that, no one is "forced to consent" to anything as this is all open source code. If you notice from the letter, the concern is actually the opposite, it's about about downstream forcing their untested themes on some GNOME apps without concern for the app developer, which is resulting in bugs and unhappy users.
>The only way a user's own custom theme will be used if a proposed opt-in flag is added to libadwaita
No, this is incorrect. The opt-in flag is about the platform theme. The change in libadwaita does not affect the user's theme. User's theme still has top priority over all other CSS, this is documented: https://docs.gtk.org/gtk4/class.CssProvider.html
And you can in fact verify that it works if you have the latest libadwaita from git master.
I would like to again emphasize that even if this weren't the case, the code is open source and it would still be quite trivial to comment out some lines and install your own CSS, and that is the worst case scenario. So realistically there is little reason for alarm.