The Cleveland small block is the only one with an internal coolant bypass. Other Ford small blocks have an external hose that is always in operation.
The gap between the Cleveland plate and hat has been calculated and shown to allow a similar amount of coolant flow as the always in-play bypass hose on the other small blocks.
It was apparently never intended for the hat to completely block the passage in the plate .
It is possible that Marlin chose to make his hat to more closely fit the opening in the plate.
I do not know if there is a requirement by design for some Cleveland coolant to always be re-circulated, but that is the case on the other small blocks.
The thermostats now being sold by Tim Meyer are, I believe, an exact match to the originals.
If I were you I would do one of two things :
Contact Marlin and ask him to explain the dimensional differences. If it turns out his intent was in fact to more fully fill the opening in the plate I would be very cautious to assume that is a proper modification.
Order a new thermostat from Tim Meyer .
Hope this helps you better understand some of the issues involved in your situation.