npm, pip, etc.. are CLI install tools. jDeploy supports CLI app distribution using npm also. But the key difference is that jDeploy provides double-clickable installers for the apps. If you're distributing a desktop app, it should be installable in the desktop (IMO). Making users go to the command-line to install the app is actually prohibitive for the average user. Even when your userbase is programmers, I find that making them go into the command-line loses them.
> Does the app installed this way get more permissions coming from a signed installer? I'm not familiar with OSX security model.
Since Catalina, you can't download and run a Mac app in any form unless it is signed and notarized. Using the signed and notarized installer allows you to get around this limitation.