While I`m not completely knowledgeable of all the specifics arrived to in the way the directories have been organized as I am mostly a plugin maker, I could be mistaken but I think the -include_lib() convention is used for e3d and intl_tools so they can be used for plugin development. The other include files more likely are intended for wings alone so they use -include() instead.

Personally when I develop plugins for wings I have ERL_COMPILER_OPTIONS set to include the wings parent directory so I can build plugins outside the wings directory.

This is the same #429 I guess.
Erlang expects applications to be in "AppName[-Version]/substructure".
Handling include paths with a version to the application is trouble some which is why include_lib is used which handles that
automaticly. Now wings is a bit special since it since a standalone application instead of an ordinary erlang library.

99% percent builds wings from a git repo with the default name and works.
If you want some other way supply a PR.