You seem in your previous posts to have established that AppleScript can create the kind of bookmark actions you want. And we have clearly replied that JavaScript cannot.
And you want nested bookmarks; perhaps AppleScript cannot do that (I don't think anyone can remember). JavaScript can *create* nested bookmarks, but I can't see a way to rearrange them.
So if those two APIs are exhaused, the plug-in API is left. This can certainly do that, but will have a steep learning curve, will be written in C, and will be run from WITHIN ACROBAT, not an external script or app. You may need considerable study of the PDF Specification; the plug-in API frequently makes no sense unless PDF internals are understood.