The TrueType font format is limited to a maximum of 65536 glyphs (2^16), so no single TrueType font will be able to cover all possible unicode characters that have more than a million defined characters.
The suggestion to support generating bitmap fonts from multiple input TrueType fonts has been made before and is on my to-do list. I have no idea when I'll find the time to implement this though.
I'll consider the suggestion to allow the user to scale individual glyphs differently. Though I have a feeling that would be more easy to solve by using the other improvement. When the tool supports using multiple fonts, then you could just use the same font at different sizes to generate the different glyphs.