I use the FMP mod (forgot to say great stuff ! keep going !)
I think about something. In the starting base you can start with a "prison". It's an installation that can be upgraded to "alien containment" when the tech is available.
What's the difference: Prison can only be used to store MIB and Hybrids not aliens with no number limit.
Alien containment can also store MIB and hybrids after the tech is available but MIB and hybrids should not be counted in the facility size limit if the option limiting the size is used.