Found it. I was confusing the VP Flight Plan thingie with the VP on the map page.
Even so, it would have been a long time before I found the "Set Altitude" Option.
I hate to suggest a "Nanny" feature. (Even tho iFly already offers Alerts.) But since it appears you're already plotting altitudes and terrain, would there be any benefit to having iFly pop up a box after you fill in your flight plan that says "You're initial altitude will not clear terrain for your intended flight"? And then offer to take you to the VP Flight Plan thingie to see the problem.
(And then we could click on the collision point, which would take us to that point on the map page, where we could rubber band away from the terrain? (Nothing is impossible for the man who doesn't have to do it himself. <grinning>))