And that goes to show how much hard work people are putting into things shared here, even if it is just a theme (let alone a whole ROM).
It's the way it is, everything is connected and structured, you want to change something, you need to accomodate the change into all related aspects of the framework.
As far as your issue is concerned, it's about the "legacy" theme. Since Honeycomb and now ICS, holo theme is the default theme. Some applications however still use the old Android theme resources, including the old scrollbar which looks a bit odd when mixed with the holo theme. This ROM is a combination of stock Sony ICS beta (aka Sony skinned) and AOSP Android. Most probably this is the reason why you are seeing this glitch.
While I am the one to always look for perfection, I feel that Z should not be bothered with the scrollbar at the moment. So, I suggest that you open a new thread about it in Themes & Apps or Q&A section, so many more people, even those not using this ROM atm, can help you.
I completely agree. It's definitely not worth worrying about. It was just interesting to see if it could be fixed without a huge amount of work. Having seen the issues it causes trying to fix it, there's a million more important things people could do.
Great point for learning though I guess