Glad to hear that it is working now fine for you.
Well, I think that I know what have happened. The instructions I gave you were for an standalone edition of tiddlywiki because, well, I thought you were using a single html file.
What have happened is that you have restarted your server, and that is the equivalent of saving the TW standalone twice. You gave TPouch the opportunity to inject the required code on the head of the page, and that is why it now works.
This is what I warn you about. TPouch is a sync adaptor. The current mechanism of tiddlywiki only accepts one single sync-adaptor, and the one with the highest precedence or the one added the last wins, in this case it is the pouchadaptor. So even knowing that you have the filesystem sync adaptor and that you are running a node TW version, the pouchadaptor still wins an gets the monopoly of handling tiddlers.
Not necessary. Yes, new tiddlers will be saved to the database, but that does not mean that you can not load .tid files on startup. When you start your node edition of TW it will load all the tid files inside the tiddlers directory. Then, when you edit and save them on tiddlywiki new versions will be saved to the database. So you can understand your physical tid files as the first version and new revisions will be stored to the database.
There is nothing wrong with injecting JSON tiddlers on the database tough, they will be loaded fine too.