I went back to watch Unleashed’s cutscenes after Frontiers, and it doesn’t contradict anything. The Gaia Manuscripts tell of one time that Dark Gaia appeared thousands of years ago and the temples were used. It’s later that we learn the cycle has been going on for the planet’s while life, which means that the temples, which can harness the emeralds, have to be a newer development. The thing that bugs me a little is that the ancients bringing the seven chaos emeralds to the master emerald and presumably building the shrine (or what would later become it) seems like it’s meant to lead into Sonic Adventure’s backstory, but countless other civilizations used the chaos emeralds in between then. It’s not actually a plot hole since the emeralds just end up scattering all over the place anyway and it’s not weird for them to return to the master emerald at some point, but it would be a better connection to SA if they’d just stayed there.