if your daughter is currently in Bali and has no flights booked, she could fly to Kuala Lumpur (cheapest of the other local 'big 4' air hubs) and get her single entry tourist visa from the Thai embassy there. May be an easier experience than Jakarta if she has not been before, and likely to cost a similar amount for the travel expenses. Plus she could enjoy Malaysian food for a couple of days while she gets through the visa application and collection process, a refreshing contrast to the also-delicious Masakan Padang 😉 "...wants to run a business there" In Thailand? Or remotely from Thailand?
may I ask: they know because both were presented at that entry point, because both were used at some stage to enter Thailand, or because "the system knows"? Thanks :-)
So for clarity, rather than bounce would it be possible to stamp out with HU passport via a Malaysian land border, enjoy Indian food and China House cake in Penang for a couple of days, then present the AU passport with SETV to the same Malaysian land border on the way back in, whether it is at the train station / walk through / or main bus route?