I'm surprised that your situation has 'flummoxed' tax agents. It's simple. The villa/granny flat/whatever is part of your main residence and as such would ordinarily attract the main residence exemption (MRE) for CGT purposes. Given this, the loss of the MRE stemming from your Airbnb activities is proportionate to your use for income producing purposes. The % loss of the MRE CGT shield is equal to the % you could (and should be) claiming of fixed expenses such as council rates etc. This amount is floor area (or total area, if land is involved) x % occupancy over the period starting when you first used it for income producing purposes and when you sell it. An important part of this calculation is establishing the value at the time you first used it for income producing purposes, so if you didn't do this at the time, it's probably a good idea to get a retrospective valuation done now. Retrospective valuations can be complicated, so don't leave it too long.
BTW, if you check your lender's documentation, I'm sure you won't find that they've somehow found a way to secure the loan only against that portion of your property, so I'm not sure what you mean by 'separate' mortgage. If you want greater certainty about the proportionate deductibiliy of your mortgage interest and the treatment for CGT purposes I suggest you apply for a PBR. The process is free and very straightforward. All the info you need is on the ATO website. However, you shouldn't need to do this as any competent accountant should be able to explain it to you.