Other than the one wire connector and the IR, most phones have all the same hardware and much more compute power, there is nothing stopping a rooted phone from doing the same thing. The Flipper is just an easy UI on a cool form factor.

It sounds like a lot of the thefts work based on the principle of amplifying the fob so it seems close to the car even when it's not. Because all reasonable EM radiation can be amplified, there's no simple way to beat that short of going back to requiring a fob button push, so it's basically convenience vs. security.

They could try fobs that are smart enough to guess whether they're being handled normally when activated, but that will 100% annoy consumers any time they try and do something the software doesn't expect. It could even get as bad as the consumer putting the fob on a flat surface in another vehicle, and gently driving it up to the vehicle they want to move into.