What could the discolored areas on the underside of my roof be?
I doubt if it's mold, but don't trust me or any other so called expert. Have it tested. 

The dark areas seem to be along plywood joints and not in "irregular splotches". Mold tends to grow in random shapes...

However, it appears there is a lack of attic vents. There should be vents along the eaves and I don't see any daylight along the eaves in the picture. When moisture gets in the attic and then condenses, it will form on the plywood sheathing. After a few years of this it will discolor the plywood, especially at plywood joints (where there is less resistance from outside air to attic air) and around roofing nails. Are there dark areas around protruding nails? 

Mold can form anywhere, but I think this is moisture and a lack of ventilation.