> a) Top-level 'make install'/'make package' commands should
> create an entry in some database.
> b) Lower-level 'make' commands should not create this entry.
> Presumably, the top-level 'make' would create an environment variable
> as a flag.
> c) When a package is deleted, its database entry is deleted.  

Is this related to "pkg_info -u"?? (Compare with output from "pkg_info 
-a".)

Have a look at your package database +INSTALLED_INFO files for 
"automatic=yes".

Maybe that does what you want or can be extended to do what you want.