Except for all the texture, clipping and transparency problems described here: http://shenmuedojo.net/new/extras/s2xboxvsdreamcast.html
The Dreamcast version of Shenmue II is the definite one (except for that Out Run cabinet error).
Some of those differences aren't even bad or a negative. There are benefits and drawbacks for both versions.
Extreme downplaying. There's a lot more issues and that list from Shenmue Dojo isn't even full. The person who complied it just gave up after finding those issues because it was time-consuming and hard on his eyes. The underlying fact is: the Xbox version is not definitive and many fans don't want a version with glaring issues like the fans clipping through metal bars.
The graphical effects from the Xbox version can be turned off, but the problem is that they might not add such an option. Of course, PC modders will hack it, but the console owners might get stuck with them. We need to voice our concerns and nobody should downplay things just because they personally don't care about them. It's all about providing the best product in general.
The remaster is needed mostly because DC hardware is failing due to old age, not to mention the problems and costs of upscaling SD graphics on modern screens.
I don't think glaring is the most accurate way to describe these differences. Glaring would be in your face where the vast, vast majority of people would never know about them unless they were shown or looking for the differences.
Also it's 2018, they aren't going to use QAA. No need to be that worried because they are using the Xbox version.