I wouldn't be so sure. Automotive acoustic engineering is one of the biggest segments of the acoustic engineering world, and car companies do put a lot of time and energy into the acoustic environment within the car. After all, if you are going to make a million of something, it's certainly worth a bit of effort to design them correctly*.
And Toyota is known for good/thorough engineering. It's no accident that my brother's 1997 Lexus is still going along heartily with >200K miles.
On the other hand, weak bass being filled in by road noise could easily be a coincidence, something inherent to the nature of low frequencies. But I wouldn't be surprised if they did tune things based on the road noise profile, either.
*This also makes me think... very few high-end audio components are produced in quantities that most mainstream cars are. So this means that pretty much any Toyota is technically a more popular stereo system than whatever we have in our homes. Odd to think about it that way...