I see dragonmarks as the exception to IH magic. Beings with such marks have had a piece of magic bound to their bodies and souls, making that particular type of magic reliable and easy. Heck, this perspective even allows you to keep the per diem limits of dragonmarks in IH's per encounter mentality, as their bodies and souls can only safely channel the magic a few times each day.
The only real problem with D&D magic and Iron Heroes is all those magical items that are meant to compensate for the fact that your character sucks without magic. Iron Heroes don't suck, so rings of glibness, cloaks of elvenkind, rings of protection, cloaks of resistance, belts of strength and the basic issue +1 sword can all disappear. Cool items such as flying carpets, airships, Holy Avengers and bags of wind can stay.
Remember, actual spell casters are very rare in Eberron. Unlike the Realms, 95% or more of the NPCs have actual NPC class levels. Only Adepts and Magewrights have any casting ability at all and both are
much weaker than a D&D PC caster. Also unlike the Realms, most Eberron NPCs are level 5 or less. Which means that those rare NPC casters will have Magic Missile or Cure/Inflict Light Wounds as their most impressive spell.
Iron Eberron will work just fine. As soon as a decent, IH friendly magic system is found. Confused Jackal Mage may be on the correct path over in
this thread on the IH forums. It's certainly different from everything else that I've seen.