so you have a home in Australia which you don't let out, you visit it regularly and it's always available to you? Seems an expensive way of doing things. From what I can see retaining Australian tax residency is not as straightforward as many of you make out.
Your visa is irrelevant. What's relevant is the time you spend in Thailand each calendar year, 180 days or more then you automatically become tax resident. Once tax resident income you bring in to Thailand is assessable for tax, doesn't matter if you bring it in your pocket, withdraw it from an ATM or whatever. If your country has a dual tax agreement with Thailand you can claim a pro rata credit on the tax already paid on the income you bring in
Your employer should make it very clear in your contract that you can only work for them and that you can do so remotely from Thailand. It should probably also stipulate that you can't work for or with any thai entity on their behalf and that you must ensure that nothing you do creates any relationship between the company and Thailand