The benefit of using node would be to have neatly chunked tid files, rather than wikis to search. What is missing as of yet is a parser / indexer that semantically searches tid files, e.g. certain fields, like tags or title or text, or date fields, etc.. A CLI (and possibly a ui on top) would surely majorly enhance the node experience.
Node is not so user friendly and I would need a manual to use TW in command line under Node.
I certainly see how using a CLI comes with a barrier and requires a greater willingness to learn and remember and perhaps a need to often use certain commands, to not having to constantly look up the right one and its spec.
There may be a default storage location for embedded content. However, you are not bound to use that, you are quite free to organize both tiddlers and external files in any way you find suitable to your project(s). In fact, your folder structure and the eventual titles / addresses of those tiddler sin your wiki are entirely independent.
I think on node it is much easier to manage tiddlers in whichever wiki / folder structure you want and to cross include different components into whichever build / bundle / aggregated wiki you want to eventually create.
So, the complexity of your considerations sure calls for node. Perhaps usability comes with actually using it day to day. Also note that using the node version does not bar you from working in a browser environment. It merely adds the optional steps to organize your tiddlers in wiki folders on the (server-side) filesystem.