Your comments

I could add a third button to the alert: "Don't ask again" which would disable this message if you do a quick upload in the future.
That sounds like a really nice idea. Do you have any specific gestures in mind for some of those actions? (maybe two finger up for page up or something like that)
Did you try the builtin WebDAV server? This is essentially an HTTP server that can serve normal html and css files as well as images but has WebDAV extensions that make it possible to transfer files.

Have a look at the manual to see how you can start the server: http://www.textasticapp.com/manual/lessons/Starting_the_WebDAV-Server.html
How exactly would you like to see this implemented? Should Textastic ask for a password when tapping on the "globe" button before it shows the remote connections screen?
Thanks, customization of the additional keyboard row is planned for an update: http://feedback.textasticapp.com/feedback/7441-more-key-sets-configure-additional-keys/
I thought a lot about this when implementing the quick upload feature.

In my opionion the override alert should stay:
The uploading option only appears if you are working with a file downloaded from a FTP or Dropbox server. If you didn't, the first option will be to mail the file.

So, if you accidentally tapped on the upload action, this is your last change to prevent overwriting a remote file. This can be a destructive process on a live web server, so Textastic warns the user.
You need to select the correct virtual on-screen keyboard layout corresponding to the connected hardware keyboard. (see comments)
No problem. Maybe it will be helpful to other people. :)
The keyboard layout is provided entirely by the iOS system. Did you try to use your keyboard in another app (like Notes)?

You need to select the correct virtual keyboard for your hardware keyboard. So, if your hardware keyboard is French, you have to tap on the "Globe" icon on the virtual on-screen keyboard to select the corresponding French keyboard layout.

There is also a problem with accented characters in Textastic 2.0 that might be problematic for you when you want to type French words: http://feedback.textasticapp.com/feedback/15340-wrong-behaviourcrash-when-entering-accented-characters-using-a-hardware-keyboard/
What exactly are you trying to do? You can open .xsd files in Textastic, can't you?