Yeah, the OP is overthinking this. By filling the radiator, you are filling the lower rad hose. That hose is connected to the block, and when fluid flows into that chamber, it works its way up as the water level rises in the radiator. Even with the check valve, the coolant system isn't 100% air-tight, so given enough time, the block is always somewhat full of water, just as long at the radiator is full.
It will overheat a little when refiling after a coolant flush or
t-stat replacement or
waterpump replacement. And unless you have a heater core block-off valve (like in the rear circuits on the van), you will always have some coolant flow out of the block to the heater core circuit to help siphon off the heat of the block even with a theoretical blocked t-stat.
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That is especially the case when the vehicle is idling and not under load. So it would be really hard to cause major damage to an idling IDI with a supposed blocked T-stat or block with several pockets of air in the coolant systme.
That being said, I would definitely replace the t-stat with a motorcraft t-stat like Mac said. Wince you are already doing the work on the waterpump, it seems natural to install the t-stat too. Also, buy a 2nd t-stat and put it in your glove-box, just in case you run into heating problems a few years down the road.