Just contain it and go for simplicity. There is no mention of elements or power spots in Chrono Trigger; the only things of this kind are the Rainbow Shell and Sun Stone, artifacts imbued with planetary energy (no color or anything). Chronopolis devised the Element system by dividing up the Dragon God according to colors; it was arbitrary. It then terraformed El Nido, meaning it was responsible for the placement of Power Spots (solidifying the case that they aren't natural (in the sense that they arose out of normal geo...something) and were part of El Nido's paradise). Chronopolis also apparently engineered the concept of the Element Grid for use by non-intelligent species and humans alike, and made everything compatible. The Dragonians then forged and developed them over the years. It is thought that one of the reasons Porre takes so much interest in the little archipelago of El Nido is because of Elements and their easy activation. (In other words, Chronopolis/Dragonians created Elements, engineered El Nido to support their development, and made them in El Nido for years undisturbed.)