I did not work with FlashDevelop, but yes, i know that there are a lot of editors which have different behavior and code highlighting.
Also i know that 3 most popular IDE for Java - IntelliJ Idea, Eclipse and NetBeans - do have TODOs highlight.
Actually a lot of code editors (and even some text editors) highlight some key phrases like "TODO", "FIXME" and others - TODO is simply the most popular one.
Also IDEs i mentioned before have a similar frame to the one you shown on the screenshot - with TODOs in your class/project, but that is totally different feature.
It is much better to see the TODOs highlights right in the code so you can easily spot them near some method/variable or whatever else while scrolling/reading through.
The frame with class/project TODOs might be used for other purposes but it is not a replacement for highlight at all.
Also, if such feature will actually be added into RSyntaxTextArea - you can just switch it off or simply set the color to the same color comments use, if you don't like that highlight so much of course.
So i don't really see why separate frame "is a much better solution" and why TODOs should not be added as a highlight option