Let me explain why it's important to keep OBJs in the Geometries folder. It's not just a personal preference - there is a reason for that.
Like you said, Poser doesn't really care where the OBJ is, but the runtime structure was originally intended for OBJs to have their own place, and there is a reason for that. The reason is that anything can be rearranged in the "library" folders, but NOT in the Geometries and Textures folders, because the CR2s, PP2s, etc will reference them by specific path. If we leave an OBJ in one of the Library folders (Character, Props, etc), people might rearrange them and the product will stop working. That's why stores will enforce that OBJs should be placed at the Geometries folder.
The problem is that Poser will NOT obey it's own standards, and by default will place newly created OBJs in the same folder as the CR2 or PP2. It has always been a chore to move it to the Geometries folder and fix the wrong paths on the CR2, PP2, etc. But that's something you will WANT to do to make sure people will be able to rearrange the library folders without breaking the contents. The same goes to the textures - you will want them to be in the Textures folder, outside the Library folder boundaries.
That's it in a nutshell.