Yes, it does.

You can actually just drag the icon from Textastic's window title bar directly into a Terminal window to insert the path to the file.

You need to reference files with relative paths, not absolute paths. Something like this shouldn't cause any problems:

<a href="otherfile.html">Other File</a>

Update: I can reproduce the issue, but it only happens when you have more than one tab open. I'll see what I can do to fix this.

I can't reproduce the issue. On my machine, windows are maximized when I click on the Dock icon of Textastic with that option enabled.

Which OS X version are you using? I'm on 10.8.5.

Also, I'm not aware that I'm doing anything that should prevent the default behavior from working.

I do plan to include a dark keyboard option when I redesign the app for iOS 7.

Please try to enable the "Debug Log" setting in the connection's settings screen. Tap on the blue arrow on the right side of a connection to change its settings. This creates a log file when you try to connect to the server which might help you find out what's wrong.