99 B4000 V6, leaking thermostat housing

Thermostat was bad, overheating then a bad leak at the housing. Stripped lower thermostat bold. We tap a bolt size bigger and get a tight fit on the housing, but still a leak. Even added plenty of RTV, still a slow leak.

Any chance the housing from the radiator hose is slightly warped? Why would silicone not seal this thing?

Or is this a hairline crack in the intake manifold at the thermostat? Can't see one.

Thanks for any help.