Hey there,
While you've mostly heard about Harmony remotes, the Harmony Hub fits right into the mix.
Controlling your HTPC setup with Windows 10, Kodi, and MPC-BE sounds awesome. You're correct that using the full keyboard option is likely your best bet to have seamless control over both Kodi and MPC-BE. Flirc helps you map those keyboard functions to your remote buttons effortlessly.
Oh, and don't forget to tweak your TV settings for the ultimate viewing experience!