The Minimum Connection Time (MCT) is as it says, and applicable to passengers and bags. It sounds like you are booking two separate tickets, as an airline or travel agency won't sell you an itinerary that violates the MCT.

The MCT for 4-4S for Iberia to Iberia flights is 65minutes for example. BA-IB is 90minutes.

You should also be aware that some airlines will not interline (check through) bags on separate tickets, and you would need to collect your bags at Madrid and then re-check with the next carrier. And your bags won't be interlined (or at least, the agent shouldn't let you) if you have separate tickets that violate the MCT.