Your experience tells you Apple have no idea what they are doing.
1. They have not released an update to windows for ages.. even with Win8 now out for more than a year.
2. Apple do not use FTP.. FTP is not a supported protocol on the TC or AE.. therefore it is out of sight and out of mind. It is also not a secure protocol so to some extent they are justified.
3. They provide one method of remote access which is propriety.. which requires you to sign into the Apple world. And use iCloud and BTMM ensuring you remain in the Apple camp.
I've spent 400 on Apple AirPorts over time and feel like Apple should fix this issue, considering how even the cheapest routers support FTP and it is a well used protocol.
I am sure they will fix it.. when is the problem.. since it is not a protocol Apple needs or uses.. they don't mind and you don't mattter.
Buy a alternative router.. bridge the AE and it can do all your wireless and become a shiny white switch with the ports orientated the wrong way.. at least until the next firmware comes out and you can give that one a try.