The LEGO stuff is always a bit off when it comes to likenesses, it happens. It can be pretty hard to adapt some things to LEGO's style and the occasional limitation of the minifig itself. That's why the Season 1 Sabine minifig's shown sleeveless instead of having short sleeves, because at the time of printing that particular fig they hadn't figured out two-toned arm printing yet. I think LEGO did pretty good with likenesses Rebels figs-wise, though I still think Kanan's S3 figure should've had the mask printed on his face instead of molded to his hair, the sizing difference it caused made it look pretty goofy.
And the Grand Inquisitor did indeed wear a helmet in Empire Day, while piloting his TIE Advanced v1. I can't remember if he wore it after that, though, I think he might've later in the season. It's been a while since I watched S1. :)
Well, yeah, but he's not much better looking in animation format either, so I think it all works out.