The bit of the exhaust downpipes I retained for my M54B30 engine on it's stand is similar. The pipes are seemingly random dimensions and appear to be a mix of stainless and mild steel welded together. I noticed this when trying to decide where to chop them and weld in some off the shelf bends to make a short system for running on the stand.
I have wondered about my custom manifold. The length and internal dimensions of the pipes from each cylinder are the same as the original cast piece but the merge on the 2-1 part of the down pipes happens sooner than it did on the original and goes to a larger bore. The original M50 exhaust (below), being for an engine management system with a single O2 sensor, merged to a common pipe anyway, unlike later designs, so I don't think it would have a massive effect
I think the science behind exhaust design, header lengths etc is more about getting noticeable gains rather than causing noticeable loss. My E46 325 is two completely separate pipes all the way to the back and it similarly doesn't perform well until you get the revs up.
I think it's really just down to perception more than anything. The BMW straight 6s are known for liking revs rather than delivering low end torque. I'd just assumed that with the weight gone, that constraint would be magically removed. In most peoples minds it would still feel really fast, I just have high expectations. Like Mike says, I've probably just got used to the M3 but with the lack of rev range on the Marlin, it feels like you're having to rag it to get the performance out of it.
Acceleration vs noise will also have an impact as I'll be associating lower rev loud noise with what would normally occur much higher up in the rev range on a normal car so my ears are telling me it's time to change gear when I'm barely past 3000rpm. The (as it turns out) useless layout of my dash means I don't easily notice the actual engine speed either.
As I've only done about 30 miles so far, it's too early to call, I need to get used to it. The weather the last few weeks means it's been sat in the garage. Last weekend was dry enough but it was 2 degrees out of the wind so I had no intention of going out in that.