Comment on SharePoint Server 2016 patching using side-by-side functionality explained by Stefan Goßner

Hi Dan,
its not exactly as you mentioned. The patching is only done in the layouts folder. PSConfig later copies the current JS, CSS and HTM files into the new created “version” folder. So of course the version folder will have those files after the update.
Without solution update you should not have to care about this as SharePoint ensures that the JS files are taken from the version folder and other stuff is taken from the layouts folder. Only if you are updating your solutions outside of a CU update (I know many customers use the same maintenance window used to install CUs to update their solutions) you would have to take special care to ensure that the updated files get copied to the version folder. Running copy-sidebysidefiles willl do that.
Cheers,
Stefan