I hear you, and its similar to what I have seen with other software. I see the benefit to simply targeting a folder directory and loading something. Though I put some thought into it and have good reason to do this differently.
Consider this. You buy a 3D model online and when you import it into your game engine, the file has weird names. Textures are not correctly mapped to a material etc, and you have to clean things up. With the next release, you will be able to rename individual components of a 3D model. That way when you export it is in line with your own naming convention, right down to geometry, textures and material etc.
I will however bee adding the feature to do a full export of the database, either to a single DB file for transport or broken up into folders with each asset exposed. So if someone decided they wish to no longer use the app, all the files are handed back over in a usable manor.
As for the Server, an indie-dev would not notice the difference. It will be able to install on both Server and Desktop. During the initial setup, the user will be able to set an option to make it public or privately accessible. If private for say an Indie-Dev, they just go so a URL like localhost:0000 and use as normal.