Well, having a cover naturally tames things a bit, so Tim adjusts the wind of uncovered pickups so the sound difference is virtually negligible. I haven't had a chance to A/B two identical pickups, one covered and the other uncovered, so I couldn't be sure. Some say that uncovered pickups have a sort of "openness" to it, but I think changing capacitors or using a higher-value volume or tone pot would have the same effect.
But to just get to the point: no, I don't think it would be vastly different. Slightly different, yes, but not vastly.