No, is the simple answer. The Mark IV foot switch will simply turn on/off the loop itself, regardless of what is running through it. Meaning, you could have both pedals on, and then when you hit the FX loop switch, you would get both effects on simultaneously. If you want to switch them off/on individually, you will have to use the pedals themselves or some sort of midi switching and then an interface/loop, like a switchblade, or the like. There are many options these days.
Then, you can program the interface to include each pedal individually, or have both, or bypass them depending on your needs. I used this method with my Mark IV and a Rockman Midi Octopus w/ Remote Loops for years. Everything on the Mark IV can be midi switchable via the jacks on the back. It is a great way to do what you need.
Hope this helps...