The article notes that their system specifically delays the challenge/response by nanoseconds vs. milliseconds by staying in the analog realm because doing a A/D -> Tx -> Rx -> D/A sequence added too much delay.
This implies either the car security system either measures the challenge/response delay or could measure it in which case this MitM attack still will work since attack's nSec delays will be very difficult to detect.
Most relay attacks require the signals to be converted from analog to digital and back, which takes time. The researchers were able to keep the signals in analog format, which reduced their delay from microseconds to nanoseconds and made their attack more difficult to detect.
No crypto is broken in this scenario.
EDIT: I understand now, having read more carefully, about how this particular MITM attack works. Nasty. The only solution would seem to be to give up some convenience.
If I made cars, I'd make sure I'd solved this problem on my products, then buy some TV adverts showing thieves in carparks bumping other manufacturers locks wirelessly with ease. Perhaps backed by graceful classical music. Try and make it look like the advert was bought by my rivals and aimed at car thieves.
Although that might be asking for it...