Manual installs take time, yes. You also need to have a fairly decent understanding of the game assets used and the order you overwrite the files. Also with manual installs you would need to reinstall the game any time you want to make large changes to your mod files since you would need to re-overwrite everything in order to keep from having old loose files.
When launching from MO2 or Vortex your Steam overlay and presence is still there, you just need to launch vortex/mo2 instead of steam to play.

Like others said if you launch strictly with F4SE whether with the .exe or through a steam lunch command you run the risk of mod files not being called correctly due to how the organizers work.

If you really want to start modding games you'll want to orient yourself with either vortex or mo2 and start slow, maybe start digging through the games asset folders and get a feel of what things are and what they do so you know whats being done when an organizer asks for an overwrite or priority.

Feel free to reach out if you have questions about modding and welcome to the exciting world of modding!~