I think bindurl and unbindurl would solve most of your complaints: if you just want a few Tridactyl binds use blacklistadd then `:bindurl [URL] --mode=ignore ...`; if you want just a few webapp binds use `:unbindurl [URL] ...`.

There's also Ctrl-v in normal mode that lets you send one key sequence to ignore mode - I use it on YouTube with `Ctrl-v f` to toggle fullscreen. Ctrl-o works similarly but for normal mode from ignore mode.