Thank you for the clarification! Yes projects would need their dedicated place somewhere in the hierarchy. Maybe bookmarked or linked for quick access.
I initially thought Roam is something similar to Dynalist but now I understand it’s something completely different.
My personal opinion is, that if the user thinks trough his hierarchy and makes up a good system it takes next to nothing to put in everything at the right place. But admit that this is strongly depending on personal preference.
Edit:
In Roam you use a single page to store all your notes. This page for me in Dynalist is a bullet in the hierarchy and I store every new note (tagged and with references) under this bullet.
My hierarchy is very simple and I can move every new not really fast into that hierarchy.