StripState markers protect content that need to be protected from further "wikitext processing". So, where the return value from Parser::replaceValues has strip state markers set, Parsoid needs to actually tunnel that content through rather than unwrap and let it go through the rest of the Parsoid pipeline.
For example, some parser functions might return HTML not wikitext, and where the content might contain wikitext characters, we are now going to potentially mangle that output.
The reason we haven't run into this so far seems to be because none of the extensions deployed on the Wikimedia cluster register parser functions whose return values have the "isHTML" flag set.