Currently, a special case for a non-zweo stub-threshold is implemented in WikiPage::shouldCheckParserCache. It would be more logical to either have Parser mark content as uncacheable if it uses a stub threshold. Or to have ParserCache maintain a list of "cache breaking" options, that we don't want to vary on.
The background is that the sub threshold can be any arbitrary number, so it can potentially fragment the cache by a large factor for little benefit. The option seems to no longer be present in the preferences UI, and has long been proposed for removal, see T30426: Remove stub link formatting user preference from MediaWiki core.