I never quite solved this problem as thoroughly as I would have liked, but it seems to work.
According to various documentations a subsite of a WordPress Multisite (WPMS) can be assigned a default directory under which its content will appear. This would be handy in analyzing access_log files, as it is not always obvious which site is getting pageviews. This is especially true of the sites’ top index page. The problem with creating this subdirectory through WPMS’s Site Install process is that it creates an infinite redirect loop, probably on account of some .htaccess and/or cookies vagary with which I am unfamiliar.
Though not as righteous as figuring this out to its core I had a eureka moment. Just go to sites’ Settings -> Permalink screens and create custom structures that begin with the desired subdirectories. Much easier than wrestling with .htaccess and whatever other symptoms lurk beneath this annoying problem. It is not foolproof, but at least now I can tell which pages and sites are getting what traffic at the access_log level.
