Mines seals just fine with just the factory seal also.
Another common problem area on these cars, torque value is in the inch pound region, I think its 86in/lbs to be exact, and seeing as they are M6 bolts threading into toyota aluminum, they tend to strip out quite easily. When this happens, the bolt gets installed for the last time, seemingly looking like its fine nice and flush, but the next time you take it off, it will not pull the thermostat housing flush up against the water outlet housing. This is where a helicoil and a steady hand comes in handy. Helicoiling an M6 is a hell of alot easier than an M10 let me tell you.