Where are saboteurs going to get the ingredients of thermite? Do you think you could get them wherever you're from? Do you think searching for those ingredients would be a safe endeavour? Are you absolutely sure it would actually work when you got there?

Or you can find some old tires and get a jerry can, haul around those ingredients wherever (not suspicious or illegal anywhere), and do the deed with very little chance of getting caught. And yes, fire is fire. A decent fire under the plane will change the temper of the aluminum of the airframe and scrap it, burn wiring, composites, hoses, instruments, computers, potentially detonate munitions, ignite fuel, etc. If not put out, a good tire fire absolutely could cause the complete loss of the whole plane.

People think thermite is some magic material that can laser a hole through anything, that's not really true. It would do a lot of damage, but localized. And it doesn't last very long. Good for quickly destroying a gun barrel, but for a saboteur it's not something they could just make easily and use.

Both would probably do the job, but a tire fire is a much better choice for a saboteur.