Yea dude a few people like to do that kinda thing. Autos tend to send the taproot straight down and then spread the roots out. So make your seedling soil at least half depth.
You could also try using a something like a 5 inch pipe in the middle of the pot ,fill the hot soil around it the pour the seedling soil down the pipe then pull the pipe right out and theres no containers to worry about restricting your roots