I have my Eco-Complete substrate covered with regular gravel, it's a bit of a waste of the Eco-Complete but I wanted the CEC properties of it while retaining the ability to have the look I was going for.
I would hardly call fish poop "goodies", more of a pain, and with pea gravel it will fall between the gravel stones and become harder to vacuum out, which will probably lead to higher TDS and more algae problems. If you're willing to allow the gravel to mix with the substrate over time then I don't see any issues.