I believe Apple never used the blue convention on their MacBook Pros. I think they even mocked the competitors for uglifying their devices this way. Hell, I’m writing this on an rMBP with USB 3 and it uses a white plastic bit.
I think it's fine in that case, since Macbooks never mix USB port types. As far as I know, all the USB ports on any given Macbook have identical capabilities, so there's no need to distinguish them visually. You just need to be informed when you buy the device what port type you're getting.
That difference in Thunderbolt bandwidth is annoying, but there's no standard color or symbol to indicate it, so marking the port would at most vaguely signify that some difference exists, which is less useful.
Apple has never shipped a laptop with both USB 2.0 and USB 3.0 ports, which is what the blue convention is for.
I mainly meant that all the slots spoke the same protocols. So anything that works in one slot will work in every slot. However, I wasn't aware that the speeds were different, so thanks for that information.