It's a challenge for sure, and the need for more expensive micro motherboards ... The best budget Mini-ITX case is the Hyte Revolt 3, as it's reasonably priced for a small and handy chassis.

Case manufacturer Flash Scale has announced a new ultra-compact Micro-ATX chassis resembling the size and form factor of Mini-ITX cases, as reported by IT Home. Known as the G300 "Mini Cannon ...

It supports Micro ATX motherboards including back connect, large graphics cards, 360mm radiators, nine 120mm fans and ATX power supplies - all packed into a small form factor.