I haven't found it to be more difficult to engage my back when bending at the waist. I don't know why you do find it to be more difficult, so I will make a guess, which may be off base. I think it's important to maintain your center of mass over your feet when you bend at the waist. I do this by thrusting my hips out in the opposite direction that I'm bending, and if necessary, bending my leading knee, so my center of mass stays over my feet. I first noticed this in a picture of medieval archers shooting down from castle walls. At first it looked odd to me, but then I realized the artist was actually making a pretty accurate rendition of how people should stand when they shoot down.
If I were to bend by simply leaning over, my center of mass would be out in front of my feet, and I'll bet it would be harder to engage my back.