There’s nothing to stop you doing that now.
Just insert a few empty glyphs after the mapped glyph and store the (unmapped) glyph variants there.
You can easily strip out all the unwanted glyph variants later by Font, Sort Glyphs. All of the unmapped glyphs will be moved to the end of the font.
Take a look at any commercial font with OpenType features such as Palatino Linotype and you will find a whole load of unmapped glyph variants in it. These variants are accessed by using an OpenType feature called Glyph Substitution (GSUB).
For example, the ligature Th is not mapped to anything, but if the user types Th in an OpenType aware application, it will substitute the ligature for T+h.