We've got 4 Prusa MINIs running 24/7 at 3D Upfitters, and the only thing keeping them from being a perfect print farm machine was the side loading filament. Thankfully Prusa designed a new base with filament spool storage underneath, which was a big improvement. Still, it took four iterations of different changes to the enclosure before I was happy with it.
It's not just a matter of making the enclosure taller to accommodate the base. It has to support both the Prusa with and without the base, which still making it easier to slide the filament spools underneath.
I ended up lowering the front door scoop was to make it easier to insert the filament and making the entire enclosure a little larger to accommodate the wires that can stick out at odd angles. Those customers who don't care for the base can still feed the filament through the side door.
One thing that didn't make it into the final product iteration is an extension cable for the display. The cables I sourced have a flaw somewhere that keeps the display from working correctly. There's a slit in the side for an extension cable should you be able to find one that works.