Can be done with FontForge. Open base font. Element → Merge Fonts. Test saying no and if that doesn’t work well restart and say yes. Repeat for any languages you want. Then File → Generate Fonts to get new font of merged glyphs.
You can then extract unique characters from your game and use that char list in your .font to only include glyphs that are actually used in game. This thread mentions some methods Scan text for unique characters (for Chinese, Japanese, Korean fonts)