702.25d The phasing event doesn’t actually cause a permanent to change zones or control, even though it’s treated as though it’s not on the battlefield and not under its controller’s control while it’s phased out. Zone-change triggers don’t trigger when a permanent phases in or out. Counters remain on a permanent while it’s phased out. Effects that check a phased-in permanent’s history won’t treat the phasing event as having caused the permanent to leave or enter the battlefield or its controller’s control.
I don't think this is a problem because they don't use phasing to trigger comes-into-play effects, but only to change the color rules. This is clever because you can keep both parts of the machine, head and color, from interfering with each other.
A more glaring error is the usage of Time and Tide together with comes-into-play effects. At least earlier, comes into play effects did was NOT triggered by phasing.
I stopped playing a few years ago, so they might have changed that rule though.