I hear what you're saying RonDsy, but the detail of most of that stuff is going way over my head. You bring up many other issues that I have no doubt are indeed valid, but the finer details eclipse my understanding. You clearly have developer level concerns; I think I understand what you are saying, but I can't be sure.
The the_content issue didn't directly apply to me; I was interested in the plugin that is referred to in what you linked to (above), but I hadn't gotten it yet and based on the other bad press that the page you referred to gives, I don't think I will. I was more interested in WP SEO being accountable for doing something or not doing something. For the level of my understanding (non-dev), Joost did that to my satisfaction.
When I communicated with Joost, it was by twitter (@yoast). I was surprised that he responded to me. Have you tried bringing your concerns to his attention? He first advised me that if I felt it was a bug, I should open an issue (I think he meant raising a support ticket on his site). When I told him I didn't consider it a bug and I was just interested to know why it wasn't implemented in WP SEO, he gave me the response I have passed on to you. Raising a support issue might be the way to go if you think it is warranted.
Another thing. Joost made it clear to me that the issues raised in this support area are not of immediate concern to him. That should be clear by the number of threads that have 1 as the number of posts in them. If you have something that warrants his or his developers' attention, here is not the place to get it responded to. I suggest going to his site and hopefully, it will get the attention it deserves there.