Came across your concern while browsing through forum posts today.
Is your concern solved now.
If not, though I am not from the product team, I can try getting in touch with concerned folks to get it looked into.
Let me know.
I haven't found any solutions to my problem, I am interested in any insight that you or anyone else might have.
First of all, remember that Extension Builder 2.1 only supports building Flash based extensions which have been phased out. If you are building extensions for Creative Cloud and beyond, you should use HTML5. See more info here: Introducing HTML5 extensions | Adobe Developer Connection
The installation is probably failing because you have some leftovers from a previous installation. The installer will detect if you have Flash Builder 4.5 or Flash Builder 4.6 installed (NOT Flash Builder 4.7). If it finds that you have Flash Builder 4.5/4.6 installed, it will attempt to install the plugin on top of it. If it does not detect Flash Builder 4.5/4.6, it will install Flash Builder 4.6 Premium.
I highly recommend you look into the new HTML5 extensibility. Here you can find tons of resources: Adobe CEP Resources by Adobe-CEP
Thanks for your help that makes perfect sense. Is there any possibility that in the future place builder 4.7 will support the extension builder 3.0 SDK?