While the MiBox does have an IR receiver, I noticed it had a noticeable delay and sometimes would register a button press twice when using my Harmony hub, but using the bluetooth remote it came with worked perfectly. You can connect your Harmony hub to your MiBox through bluetooth if you add it as an Asus Nexus Player. When you add a device, choose an Asus Nexus player and then when you get to the step to pair it, just go to bluetooth settings on your MiBox and it will pair. Now my harmony hub remote works great with the MiBox using a bluetooth connection.
Can you try adding the Mi Box to the Hub as a Fire TV? In the past, I had heard about people adding the Nexus Player as a Fire TV, which enabled the use of the extra buttons that Fire TVs have that Android TVs don't, such as the menu button, which is useful for apps like Kodi that make use of the menu button.