You are correct...The ES-5 and 8 totally do this. I have the 5, but if you have the room for an 8, go for it.
I haven't been utilizing the FI in this yet, but have indeed used it to combine preset patches on other midi-pedals with standard pedals for patches or 'scenes'
For instance, I have a song that goes back and forth between just a chorus pedal and a patch that has chorus but also envelope, fuzz, volume swell and (MIDI) Strymon Timeline set to a delay with 5th/octave.
I have another song that triggers fuzz/envelope then a tape delay emulation. But yes, you pick the pedal (midi channel) and which patch/setting you want on it and program that in and save it.
You also don't have to put the MIDI pedals in any of the loops if you place them carefully. For instance I have my Future Impact placed before my ES-5 and then the Timeline (delay) and my Atmosphere (reverb) after the ES-5 which are where I'd place that stuff in a traditional setup without a switch/loop system. The only thing you lose by doing that is the ability to move around the midi pedals in your effects chain (the Boss units allow you to change loop placement at will).