If you have projects with different settings, I would create a new Toolbox for each project. However, if your projects are similar (i.e. use the same technology stack), I would just create one toolbox for all of them with just the low level part of the stack inside of it. I do Rails development, and I keep Imagemagick, Ruby dependencies (cmake and others) and postgres-devel and vscode inside the Toolbox, and keep the rest contained in project folders in my home directory (outside of the Toolbox, but accessible by Toolbox). I also keep node itself outside, with node and yarn installed with Volta in my home dir. See this thread: Options to install node.js on fedora silverblue
Postgres itself I run in a separate podman container because systemd services are the only things that are problematic inside Toolbox. I don’t know enough about how Mongo works to say what’s the best solution for your needs.
This way I get access to all the necessary tools without flatpak spawn and I avoid the issues you get with sandboxes and IDEs. Very happy with this “intermediate” container setup - having full access to the host while still being able to just podman rm toolboxname hits the sweet spot between ease of use and containerised workflow, in my opinion. I used to use Vagrant, but this is faster and better. I also wrote an Ansible playbook for faster setup of the Toolbox.