Soooo....yeah, to this guy here it still feels like stuff is "all over the place" 
It probably is, since you have been doing that, for years.
Therefore, I am curious what strategies (if any) have others developed to reconcile this stuff and create a better, perhaps more consistent configuration?
The EASY way, is to do a new ArcaOS install, and never do anything on your own. Let ANPM do it properly, for you. If you do find something that needs special stuff, put it all in it's own directory, and add paths to the END of the path statements, so that the proper stuff is found first (actually, that isn't true, because ANPM insists on the .; entry first, which tries to load things from the working directory. IMO, that is not a good idea, but others seem to think it is a good idea. If that doesn't work, remove the added paths, and use the Environment tab in the program icons (part of DragText - READ the instructions). You may also need to use LIBPATHSTRICT.
You can spend a lot of time trying to fix past sins, and still not get all of it. So far, I have not found any reason to add my own stuff, but I do use the Environment tab for a few things (not because of YUM). It can help to shorten the paths, by using a custom PATH, and BEGINLIBPATH/ENDLIBPATH adds to what is set in LIBPATH in CONFIG.SYS.
I let the installers do all things for me.
That is the only safe way to do it. Theoretically, whoever built the installer, knows what is required, so it does it right (sometimes, that isn't exactly true, and sometimes, old installers don't know about newer requirements). One of the things, that old installers, will do, is add the PATH and LIBPATH statements to the beginning of the lines. Anybody who is building an installer should put the new stuff at the end, so you don't break something else. There is something wrong with your package, if it really does need to be first.
After the ArcaOS installation, I point UNIXROOT to another drive with existing trees for \usr, \var and \etc.
I was doing that, so I could share the RPM/YUM install with another boot drive. I quit doing it because it was becoming an administration problem. There are just too many things that RPM/YUM does to individual boot drives, and sharing only knows about the boot drive that is active when you do the updates. It wouldn't be a problem, if you don't share with another boot drive.
Additionally, you really should point the installer to the existing drive, so it can do the necessary updates during install (especially if it is an UPDATE install).