Ssgbryan - You are probably fighting a battle that you cannot win. It is almost like a clash of right brain logic against left brain logic. You have vented, but you are likely destined to continue performing your own reorganization.  If you concede this, why not take it one step further ? As long as you are text editing a product:

PP2014 allows any Library file to load from any Library category.

Most products have a 1:1 relationship of OBJ:cr2/pp2/hr2    PNG:product  pz2/mc6/mt5:product   PMD:product   INJ.pz2:product

Make a unique Libraries folder for each product.  In it = cr2/pp2/hr2 , PMD , OBJ , readme

Make a subfolder for Material poses (because there are usually so many).

Make a subfolder for Textures.   If there are Material poses, make the Textures folder a subfolder of the Material poses folder.

Use relative paths. 

For the OBJ,  the path =  ":NAME.obj"  

For the PMD =  ":NAME.pmd"  

For textures  =  ":Mats:Tex:NAME.png"  for the cr2 etc  and  Material poses =  ":Tex:NAME.png"

I found that relative paths go down stream just fine, but do not like going parallel, which is why Tex should be under Mats and not beside it.

Doing this makes the product very portable.  The Geometries folder is very lean.  The Textures folders is very lean.