Gonna be blunt here, all of this sounds like not your problem. If his scooter gets stolen or keyed or whatever because he left it out front that’s not your problem. If it becomes unusable because some rednecks fucked with it that also isn’t your problem and it’s what renter’s insurance (and possibly a security camera) is for. If he doesn’t use his car enough that isn’t your problem either. These things may frustrate and annoy you, but they aren’t your problems because you aren’t responsible for making sure your roommate lives his life ‘correctly.’
It sounds like he got exactly what you suggested, but shaped like a scooter instead of a motorcycle, because any ‘motorcycle’ that doesn’t go fast enough to require a license is going to top out at around or under 30 mph (depending on local laws). It’s not going to be any safer driving on backroads in something shaped like a motorcycle vs a scooter.
In short, no, I don’t think that not putting the scooter in the back is something he’s doing because he’s autistic. He’s probably not doing it because there’s no pressing safety reason to do so and because it’s slightly more inconvenient.