I think in theory, the assemblies are supposed to have the same stats regardless of the order of the mods. This was the intention circa 0.9.9.6. In the previous release, that was not the case.
As for the Wiki, I'm not sure how accurate the data is, since it is completely community driven. What is currently lacking is some kind of release-related information, so there could be a mix of both old and new data.
Any assemblies that are behaving differently due to the ordering of the mods are deemed as bugs and should be fixed in the repo, I think.
There are however some instances where the order does matter. This has to do with how the mods and items interact. For example, it is generally not possible to slap on more than 1 of each mod type for boots/armour, so things that require double adding of the same mod will have to come nearer the last few mods added, or if there're exotic mods like Nano or Onyx, those will have to go on before some of the other mods.
In short, the assembly system is still a little inconsistent at the moment. Hopefully things will be completely resolved come the next release.