IMO, if your online application is a static multi-purpose application, and cannot modify itself based on the type of loan, or purpose of loan being applied for, the bank is opening itself up for significant compliance risks and penalties at some point.
I certainly would not want to tell the story to my examiner, "Well you see, the customer just didn't know better to leave it blank...". Inadverant should be far and few between... you state: "...applications and often incoude the GMI...", which tells me that the good ship inadverant has already set sail.