Uncomfortable isn't the word. But it's detracting and very noticeable to me. Firstly because it wasn't there before, and secondly because of how surprisingly smooth the first half of the layout is compared with before, rendering it jarring by comparison.
I've ridden Nemesis more than any coaster on the planet, many times in a row sometimes, over a period of 28 years. So I've got very used to the layout, hence why I never had the "headbanging" problem because I knew, without thinking, the exact moments when a sideways jerk was likely to push my head to the side and I was instinctly able to brace and avoid it.
The rattling noise is very loud, as it's right above your head. Now that it runs far quieter on the rails that before, this is the loudest noise you hear when it occurs, so I'd be very surprised if no one has noticed that! As many have explained before, this shaking isn't "rough" by any means. It's very minor at first and I can understand why it's not too noticeable. But after the final corskscrew it's very noticeable to me. Like an up and down motion. You feel it under your seat, like being gently patted on the backside.
Other than subconsciously knowing the ride through experience, I suppose I could also be more sensitive to it because I have a bad back (which it doesn't impact, and B&M seats are extremely comfortable for me). In normal situations I go limp to avoid pain when I feel such sensations in that part of my body, so I'm tuned into it.