The process you describe here still does what they’ve been warning you about - it modifies files that Nextcloud thinks it owns (even if it’s mounted as external storage), without going through Nextcloud. Modifying the files in your Linux home folder, or syncing them with SyncThing from Windows, is exactly the same as directly messing with files in /var/www/nextcloud/data from Nextcloud’s standpoint. It will still cause the issues they warned about.
Edit: Nextcloud docs aren’t adamant that problems will occur, but says it might not always keep up to date with external storages. I can say in practice that can lead to a very poor user experience, so the cron job is indeed well recommended. See Adding files to External Storages. Also, internal vs external files may have different handling when it comes to apps other than the Files app, but seem to be exactly the same for that purpose at least.
However. As long as you know you are messing with things behind Nextcloud’s back, and can take responsibility for scanning them before having Nextcloud interact with them again, I can say this causes relatively few issues. It’s not supported, but I’ve done it without frying anything.
A note on the diagram, I think the “webdav” dotted line should go from the laptop to Nextcloud, where Nextcloud then has the direct pink line to Archive on the Linux workstation - Nextcloud’s WebDAV is right alongside the GUI, as it’s all PHP. Unless of course you have a different server providing WebDAV from that machine.