I use TiddlyWiki via TiddlyPWA. It’s an offline-capable PWA with builtin sync and encryption. It doesn’t have folders but it does have nestable tags. I don’t think it supports markdown out of the box, but I’m positive you can find a plugin to use markdown. Plugins are crazy easy to install in TiddlyWiki; you just drag and drop the plugin into your wiki window and confirm the installation.
Apple’s implementation of other PWA standards requires an app to be opened from the home screen. A user can’t access features of the app if they can’t add it to the homescreen.