This amused me, and before uploading the observation, I wonder what location I should use, habitat as well.
We went out to a nature reserve the weekend with friends. After arrival, we were having coffee and standing next to the Landrover, I noticed a small Uloborus plumipes that obviously lives in its web in a secure spot at the back door of the car. So what do I choose as its location - the place where I photographed it, even if it was brought there only temporarily? Or the place where the car is normally parked at home? And the habitat - if in the reserve, it would be fynbos. If back at my friends home, I suppose garden.
Not sure what iNaturalist’s policy is, but animals use anthropogenic means of transport all the time, whether voluntarily or involuntarily (insects and arthropods on cattle or food transport, ship-assisted birds, etc.), and I think the most logical thing to do is to report an animal at the exact place and time you observe it, even if it is artificially displaced from its usual habitat. You can use the ‘Notes’ or comment section to clarify why the location may be odd for the species in question.
So many scenarios fall into a grey area with regard to where to mark the location. Had you intentionally displaced the spider, I would say it is clear you should mark the location where it was found before entering the car. That would be how to treat an observation of, say, an injured wild fox that is caught and taken to a wildlife rescue centre, or a butterfly that is caught for the purpose of pinning in a museum collection; even if the photos are taken in the rescue centre/museum, you would mark the location as the capture site, ideally.
However, in your case, the spider has travelled, albeit unwittingly, of its own accord. And, in any case, any location that you were to mark other than the one where you first sighted the spider would be a guess, since you cannot say for sure where it entered the vehicle. I would put an explanatory note in the observation comments though, with reference to the location where you suspect it was transported from.
Where the observation was made, in this case. With notes about it.
If I were to harvest something from the wild and take a picture of it in my kitchen, I would mark the location as the spot it was harvested from, rather than the spot the picture was taken, but that’s an exception.