If an MC21 is run without the fairing, except for headlight/windscreen, will the cooling have an effect on the jetting compared to when the full fairing is run?

The reason I am asking is that after a top end rebuild, I did some runs with the fairing off, and found that the front cylinder was running a bit richer than the top cylinder. Starting it the front cylinder had noticeably more smoke, and checking the plugs, after the break-in and significant running, the front is quite black, while top is nice brown, possibly a little hot.

Should running without the fairing change the cooling/jetting?