We're in our first round of IoD, and some of the Market cards there in made me pause at mixing them.
As Steve said, you can freely mix IoD Market cards into the base Market deck. The only drawback is that you will forget that the Sunplate comes from IoD, since it has no expansion marker on it.
A sad thing about IoD is that there are significant misprints that have never been corrected, which is strange considering the multiple reprints of this expansion. Once I've asked Customer Service whether FFG will ever issue a set of amended cards, but I've got a negative answer.
This is OT but worth mentioning. That answer did not keep me away from Runebound. I think this is a solid game and, while I prefer other games from this company for various reasons, I welcomed every RB expansion and enjoy a game here and there. I was surprised that there was almost no discussion about Mists of Zanaga here or at BGG; I think MoZ was an innovative expansion with great ideas, significantly more challenging than Frozen Wastes, and with a cool atmosphere and storyline. Nothing of it made it into other Terrinoth products and excellent heroes such as Maliki the Claw, Saka and Kuto, Spiritspeaker Tara ASO will never have a Descent incarnation. I don't think 2nd edition will ever include those exotic characters, not even in the Conversion Kit. What a waste of good ideas and shiny artwork.