With this mod loader you will be able to have more than 500 missions. You are able to load only a part of your mod collection which needs less than 500 missions. So the mission limit is still active, but you can easily switch between your mods.
This userdata file contains some mod information, so you will not have to tag every mod manually. Put the .bin file into your gamedata folder. If you overwrite your current ML_userdata.bin your tags will be replaced by mine, mods I didn't tag will become untagged again. Conclusion: use this file before you tag any mods. (tag = rename, e.g. CD1 becomes Capital Down 1)