If you would have read the post I linked to, you would have seen that the format name would go as an argument to the egtpath command:
egtpath nalimov D:\nalimov
egtpath scorpio D:\bitbases
Adding new formats will not require any changes in WinBoard, they an be set by the user through command-line options. The format names and what follows them is formally not part of WinBoard protocol, and can be freely defined by the inventor of the format.
The other options you are talking about are likely non-standard UCI options. (I say likely, as my knowledge on UCI protocol is close to zero.) These options are indeed a problem, but I am not sure this problem could be ameliorated in any way by uniting the protocols. The point is that you still would have to provide values for those options. If these are written in a polyglot.ini file, they are set for once and for all. If you would want WinBoard to set those options, you would have to supply the values each and every time you invoke WinBoard with that engine. Either interactively through the menus, or on the WinBoard command line as options. That does not seem like an improvement at all, especially not for lazy people!
In some other threads we already discussed how we could extend WinBoard protocol to allow engine-specific options similar to UCI. That is easy enough. The problem is how to use such protocol to any advantage.
One could doubt the need to specify too much in WinBoard protocol anyway. The protocol is mainly useful for things that both GUI and engine (or both engines) have to be aware of (to enforce consistency), and things that have to be changed interactively (during a game). For static settings, engine.ini files (or polyglot.ini files) or engine command-line options are just as convenient. Of course it would make life much easier if there was some standardization there as well.