As long as that glitch exists I would never call that lining up correctly. In fact i would say it's bad modding.

The layout of the mod looks pretty good (if perhaps a bit generic). But the placing of individual objects and attention to small details feels really messy.

For example look at those pipes on the third roof. The ends of them ar goiing inside the box object, but a bit of them is sticking out from the top. Same problem happens with the railing on the side of the same roof.

Also on bigger structures that are constructed of multiple same colour objects you have pats sticking out making the wall look uneven in a bad way. These are the cases where you want your faces to be on same level. Although even then when placed correctly they rarely need to be inside eachother.

Also one small detail that takes away from the realistic look of a mod is when you have two objects going inside each other from the corners a bit like they were melted together (see uke's side on the second roof and upper corners of the fourth building).

So I guess in short what I'm saying is: pay more attention to way you line up your object.

If you are having a trouble with thinking where the edge of your box object is exacly, you can actually take the object's length on the axis that is perpendicular to the edge and divide it by two and then add or subtract it from the object's coordinate on that same axis.