This has me confused. You can move notes around easily in Tinderbox. What have you tried—what did you expect vs. what happened. Also, Tinderbox is peerless in supporting very rich incremental formalisation.
I think the issue here is that general software use teaches us to ‘colour inside the lines’, i.e. do what the software says—or rather, think like the app’s creator. You can argue the same is true of Tinderbox, except is issn’t so constrained. It’s a tool set, not a processor. Your reference to “a specific objective or project in mind” sounds like an echo of advice given here: what are you trying to do?
If you collect a hodgepodge of notes (good description!) what do you expect? You clearly aren’t ‘just’ writing down notes. What sort of emergent structure are you expecting?
IIRC, in Obsidian, it’s actually more structured as you can only create the links using note names. Can you have standalone notes? Also playing into this question is issues is your (unstated) exceptions. Implied is that by creating the hodgepodge, magically something emerges. What is that something.
In summary, I think your confusion stems from an expectation of an (un-described) outcome. This sounds akin to the Underpants Gnomes business plan:
Phase 1: Write Notes.
Phase 2: ?
Phase 3: Profit
I recall you’ve been at some of the Tinderbox meet-ups. Today is on tagging and that might be a good place to bring this up, as in part tagging is about addressability and the ability to find things in different ways contexts. Thus structure emerges. (I do realise the meet-up are late for you - getting a mutually (in)convenient timing for a global meet-up is hard.
I don’t see Tinderbox and Obsidian as either/or, they just do things differently. Find what fits your style.