It's an interesting alternative path for refining but currently it's completely out of balance. Refining ore with crystals provide no benefits and it's more time consuming.
Omniplants work very slow and after I've built two separate paths for refining giving the same amount of raw omnite I'm making far more with Angel's path (all 6 ores fully purified) than with crystals. Do not know the exact figures but it turns out 30-50 slower and yields less ores from raw omnite. Either make your recipes more productive (which yield more ore per 1 omnite) or make them more faster. Omniplants need more speed anyway.
Also: beacons don't affect them and you cannot insert modules in them.