What are the visa and work permit options for an Australian remote worker planning to stay in Thailand for 2-3 months?

I would ask your company to soften their stance a bit and offer to do a bit of training of local staff if they will second you for up to 3 months, and you won't ask for Per diem allowance for the work

Do they know where you are working from, using VPN🤔

If your Australian company has an office in Thailand they can sponsor your work permit, and visa, as long as they have at least bt2million in registered capital for each work permit they sponsor. Depending on what business structure they are set up under, they might also need at least 4 Thai employees they pay wages, and social security on also.

To be honest no Thai company is going to help you out with a work permit for only 2-3 months unless they really need you working here for some reason, even if they are a subsidiary of the company you work for in Australia. The LTR visa for remote workers is overkill for such a short period even if you do meet the criteria

If you company's local office has Aussies working there, legally, then that office will need to do the same paperwork for you. It's been a long time but I think the process goes, you get a non-b visa, file some paperwork with Ministry of Foreign Affairs, they provide the work permit, you convert the visa to a long term visa. The process could take longer than you intend to stay.

I have working remotely while living in Thailand and not once has a government employee asked me about my work. If your work is something you can do from home (not out in the public) then no one will ask/care, especially if it's only 60 days.

You may find it easier to convince the company to soften their requirements that it is to get a work permit/visa.

Does the job require you to be in office sometimes? Do they check the location where you are (IP back tracking as an example). If they don't know, maybe just come and play dumb if/when you get caught.... Your employer will likely be more strict that the Thai government.

You can only get a work permit sponsored by a company that's in Thailand.

The only other option you have is the remote worker LTR visa. It has a high level of requirements but has work authorization built in as long as you are working for a company outside of Thailand.