I'm used to naming a file whatever I darn well please (particularly if it's just a working file) and handling it in the command line with the appropriate command without issue.
You can still do that.
If you want it to work
automatically in Windows (double-click opens the correct app), then you need to leave the extensions in place.
Way back before the Mac was more co-operative with Windows, it was common for us to receive Mac-created files without extensions. In such cases I would open the file in Notepad or Wordpad, and check for plain text at the beginning of the file that would tell me what kind of file it was (JPG, GIF, Illustrator, Quark, Excel, Word, Photoshop, etc.).