That automated atlas script looks very messy, moving UVs "by hand" isn't hard to do at all, especially compared to moving vertices in 3d space. If you need to rely on automated scripts your just putting yourself at a disadvantage.
Build what you want, and then when you 'tile' part of an atlas texture you essentially have to cut those edges into the mesh object to give the UV's something to tile on to. GeeDave, that plugin you posted a link to almost allows you to just build however you like and then 'bakes' in the extra verts at the appropriate…
I provided the script in the other thread as I wasn't sure if Max 2010 (that Mr Whippy has) had the recent unwrap features that allowed you to group and auto-pack UV selections. You can do this task with vanilla Max now though. Before the bake, using 4 separate tiling textures, unwrapped on a second channel using groups…