I understand your pain and I am sorry. Let me answer some of your questions and provide some answers and suggestions.
Adobe decided to include FlexUnit 4 in Flash Builder 4, which was great. However, when it comes to the way in which they did so, the way in which libraries are linked and the way to plugin works, we (the FlexUnit team) are only able to provide suggestions. We have no control over the approach and little ability to influence the process.
So, to be even more direct in my answer, there is no formal relationship between these two teams. What features Adobe chooses to support and the workflow/integration are purely business choices being made by Adobe. FlexUnit is purely a community project without funding or support from Adobe. It continues to evolve as we add new features and integrate contributions. Adobe may choose to increase the level of integration or to adopt newer versions as we proceed, but that is solely at their discretion.
To that end, we cannot change the way the plugin works, etc. However, we will be posting information for users interested in updating their Flash Builder version with our latest code base (and addressing at least one of your issues) shortly as we prepare for our 4.1 beta.
* FlexUnit is open source but I can't Cltr+click on things like assertEquals() to see what's going on there
>>Adobe didn't include the code for FlexUnit in builder, only the library. You can control-click on Flex classes because they shipped both the lib and code. If you do want this functionality, you can download our code, go into the build path/library path of the project, find the place where they link in the flexunit-core libraries and edit the source attachment. That will allow the control-click to work, etc. The code that shipped with Flash Builder is tagged as 4.0.0 in github.
* I visit flexunit.org, click Docs and can't find assertThat() method at all while it's available in FB's code hints (and works)
>>I will try to find out why this is not showing up and get it fixed promptly. FYI, the assertThat method is just a wrapper for the org.hamcrest.assertThat from the hamcrest library. For more info and code: http://github.com/drewbourne/hamcrest-as3
* We now have 2 documentation sets, one in the "Using Flash Builder 4" book, one on docs.flexunit.org. Some things are documented here, some others there.
>>I don't know what is in the "Using Flash Builder 4" book...if you can point me to a link I will check it out. I have no idea what is there (nor who wrote it) The official documentation site is docs.flexunit.org. It is the only one being maintained/added to by those involved with the project.
* API docs aren't even available from Adobe, are they?
>>I doubt it. They don't maintain this material and they don't include it.
Sorry if this is less than helpful, but I wanted to at least provide you some answers and context.
many thanks for your reply and the insight provided. Is the team working on FlexUnit-FB integration monitoring these forums? The current situation is not good and the feedback should be heard by Adobe.
Edit: I forgot to post the link to the official documentation:
I can't say for sure, but I believe so.