If you have a Thai visa in your AU passport will they let you out of the country on it?(Border crossing)

I cant see why they wouldt let you back in to Thailand on your AU passport? you have a visa but you also get a 30 day visitor visa on arrival?

What if you was comming in from Malasia by train for the first time?
How did customs know you were returning to Thailand on a diferent passport?

I always carry both just incase but looks like there is no point.

Den