When you use TiddlyWiki on node.js, you essentially have two copies of TiddlyWiki running.
One in the browser, one in node.js (server component), and the two synchronize with each other. The browser copy is responsible for the UI/UX and the node.js copy handles the API and saving and loading the tiddlers from disk. This is a very simplified explanation but hopefully it gets the point across.
Most plugins only involve the UI/UX in the browser and therefore do not need to run under node.js.
However, plugins that need to tweak the behaviour of the wiki running under node.js (the server component) can need to be executed under node.js to ensure they operate properly and are executed in the correct order, and therefore need to be installed as a plugin folder.
Cheers,
Saq