After submission for Australian visa passport given back
It is common practice now for the Australian VFS application center to give back your Thai passport once an application has been made in Bangkok and the reason for this is because all visas now are electronic and label less so when a visa is awarded it is on a sheet of A4 paper and not a sticky visa in the passport so do not be shocked if you are handed the passport back at the time of submission.
When an application has been submitted it is then sent to the Australian Embassy for them to make a decision and if the visa is awarded it will be placed on an A4 sheet of paper with a unique visa reference number and given back with the documents that were submitted less what the Embassy Clearing officer wishes to keep for their internal files.
This system is very modern and it means that there is no risk of any Thai passports being lost and if you ever lost your passport you could get a replacement visa at the touch of a key via an e-mail. The old sticky style visa if you lost your Thai passport you also lost your visa.