Verify that the housing is flat/true. Especially around the bolt holes, the tend to get convex from over tightening so gasket surface doesn't get clamped evenly. Try lightly sanding it on a flat surface (glass) & you should see even marks across the whole surface, if not it will show the low spots that aren't touching.
They very often get distorted. Get something perfectly flat, and some adhesive backed 180 grit sandpaper and sand it down, and that will show you the high and low spots, then you will have to use a hammer and dolly or anvil or something to straighten out the flange. Also when going back together, I suggest a generous amount of right stuff RTV on both sides of the gasket, and let it cure overnight before filling with coolant.
Generally, I would agree that a small amount of RTV is best, these thermostat housings are extremely problematic, which is why I specifically recommended right stuff, and enough of it to make sure it fills in any gaps due to the housing being warped.
This doesn't look right but is there suppose to be a dip in the bottom of the thermostat housing? Almost looks gouged or something. Redid my water pump and tstat, and no matter what I've tried it leaks from the bottom bad. I suspect this is the cause? Firs time doing this on the car since I...