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If you suspect something has failed and allowed water in, and you want to take the issue further with Isuzu, you need to have it independently assessed but someone experienced either with diffs or off-roading.
Couldn't say without at least seeing a photo, but I doubt it's anything to worry about. If you are concerned about it talk to your Subaru dealer.
Musso owners we have spoken to have been unanimous in their praise of the car. One or two have reported fairly minor issues, most love the diesel and have had no trouble at all, and many have done lots of kilometres in their cars.
Sludge build-up is a turbocharger killer, but sludge won't build up if the car is regularly serviced and the oil is changed so it's always fresh. The problem is usually only with cars that haven't been serviced. Other seven-seaters you could look at are the Kia Sorrento, Hyundai Santa Fe, or Toyota Kluger.
You are right to be suspicious when on average a car of that age would have done well over 200,000 km. Check the car's service book to see when and at what odometer readings the car has been serviced since it was new. That should give you an idea if the odometer is correct. With so little use it should be pristine inside with little wear on the seats and the carpets.
Ford deleted the spare wheel in the WT Fiesta, saying buyers preferred to have more features than a spare wheel. Instead the car came with a 'Mobility' kit, which could be used to inflate a punctured tyre to get you to a place where the puncture could be repaired.
It seems to me that they're quite different cars; the Golf R is an under-the-radar raider, the Mustang an in-your-face statement. If you want an exhilarating drive on those weekends away go for the Golf, if you want a more leisurely fun drive with a high look-at-me factor go for the Mustang. For my money I would choose the Mustang. There is talk of a twin-turbo Mustang coming as a GT500 Shelby in 2018, possibly with a 5.2-litre V8. Not sure if it would make to Australia.
Both cars meet all of your requirements, they have 5-star safety, they're comfortable, have a large boot, and plenty of power for overtaking. Either one would be a good choice, but if I were to be making the selection it would be the Toyota for reliability and resale.
The Fiesta dual-clutch gearbox in your car is trouble, pure and simple, as many other Fiesta owners would happily tell you. You could get the gearbox independently tested, but I fear that Ford wouldn't take any notice of the findings. Ford is facing a class action suit from owners affected by the problem, and I would suggest you consider joining that if you feel you are unlikely to get anywhere with Ford.
Check for possible damage that might have been done by those who 'borrowed' your car. It's possible that the battery is completely dead, but I think that's unlikely. Take it to a Hyundai dealer and have them try to find the cause of the problem.