The expert install order also should encourage people to research all the possible bugs they can run into within their installs and thus have a stable base to build a stand from which the thing grows. So if you or others(micbaldur's a good example) can fix all the bugs you run into in the current spot the mod is at, it should allow others to also use it in their games and have no longer any of the large scale bugs ... that the expert mods have.
I don't agree with this. The install order in BWS is mostly following BWP, but BWP is not perfect. Many mods have a mix of components that add content and components that tweak content. Also, some components do both. Tweak components have different effects depending on what was installed before them. Also, a tweak component can't know what will be installed after, so it's best to install tweaks later, after all content has been added. This is the general approach of the BWP. However, the BWP mostly installed components of mods together, rather than installing content adding components of a mod early and tweak components later. This is partly because BWP is (at least theoretically) a manual install guide, and installing all components of the same mod together means less commands for the user. BWS is completely automated, though, and it can easily install components of a mod separately, so it makes sense to optimize the BWS install order so that components that add content come early and components that tweak come later, even if the components are from the same mod.
In short-- I think that moving mods and components of mods to a better install order is a good thing for the modding community, because it reduces compatibility issues and means that mods are doing more of what the author intended. After that, yes, we still need to analyze conflicts and maybe change some mods to solve compatibility issues that remain.