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Crystal of Power is both a Weapon and an Armor, and per its reminder text, fills 2 slots on your character. The actual reminder text however is confusing when it comes to Megatron. It says "This occupies 1 Weapon slot and 1 Armor slot", which when compared to Megatron's ability to "be upgraded with a Weapon in his Armor and/or Utility slots" makes it sound as though Crystal of Power is overriding Megatron's ability.
This is a good example that reminder text is not rules text. It is there to help someone inexperienced with the game rather than define how a card works. It is fine for Megatron, Living Weapon, to use his Utility slot to fulfill the Weapon condition of Crystal of Power. You couldn't however put the Crystal of Power in his one Armor slot, but if you had a Utility applied like Defensive Configuration, giving you an extra Armor slot, you could put the Crystal of Power in two Armor slots.