These are two separate and unrelated issues. Let me explain. There's no question that MP3s are lossy. Hell, even the guy who invented the coding thinks they're unacceptable for critical listening. MP3s simply lack the resolution of the original media. That lack of resolution, however, doesn't change the recording's tonal balance, nor does it influence the direct perspective of its staging.
You're probably asking what all this means to you. In a convertible, you're obviously facing a lot of noise. That noise - the combination of road/tire/drivetrain/exhaust - will cause random cancellations in the speakers' in-cabin response. Those cancellations will mostly manifest themselves from the lower mids on down. IOW, it'll sound very different and significantly worse when the car is at speed. The Imprint option won't help, as the car remains stationary during its configuration. In your case, not unlike mine, the system has to be tuned while the car is on the move. This is where a PEQ is extremely helpful.
I probably don't have to explain the benefits of time alignment, as I'm sure you've listened to a stereo system where you sat directly between the speakers, and then moved far to one side. It can make for a night and day difference in focusing the soundfield relative to a given listening seat.
To recap, yes, MP3s are limited, but those limitations won't impact your tuning constraints.