A guess or wild speculation if you like
, but based on how I perceive BMD think about things, and the specs of the unit.
If you had 625 sources they'd lock to a PAL reference, and if you give the cleanswitch a Tri-Sync 1080i50Hz reference, your HD1080i50 sources would lock to that and so on....
In order to maintain allowing different video modes to pass through like a normal videohub, i.e. 50 & 59.94Hz, it would need to have some logic to use different references for different video modes it finds on it's inputs.
I'd go further to say since the product is so new, this logic is probably fairly simple at this stage, and could well advance to mean HD 50Hz sources would lock to a PAL reference in some future firmware update.
You've got a device, could you test using different types of syncs with different video modes of switch inputs & basically figure it out, then let us know - please???? Sorry to put it on you, but you sound like you've probably got the gear and expertise.