Is it better for my friend to apply for a Non-B visa in Australia or enter Thailand on a visa exempt status?

That is totally going to be down to whether the company he's going to work for can get the 90 day Non-B visa INSIDE the country at the immigration office or give him documents to go outside the country to get the 90 day Non-B visa.

I'd say IF they can get the correct documents sent to him he should apply for the 90 day Non-B visa in his country BEFORE he comes here.

Have him check the website of the thai consulate he would use in Australia for the requirements and contact his employer to see if they can get the documents to him

normally the requirements for a Non Immigrant B visa are less at a Thai Consulate than at the Immigration Office in Thailand.