I think Syncthing can be the right tool for you. Syncthing is safe and secure and transfers (as you wish) data directly.
Syncthing does not limit the number of folders or files, so you can pretty much sync everything on your computer. You only need to be careful with certain data like databases or for example Github repositories.
Please note:
Syncthing requires both computers to be on at the same time, so the data can be transferred.
Syncthing handles conflicts automatically.
The newer file wins (I think) and the other one is placed as {filename}.conflict-{timestamp}.ext (or something like that).
There is no way to do that manually, especially as syncthing has no native interface, which could pop up or something.