The alternate file manager uses NeatUpload, which works very well for us. I'd like it to be the default instead of the Javascript one or at least make it the first opened by the admin toolbar when File Manager is clicked.

I found this this old topic where it says it can't be done. Is this still true today?

Eh, disregard this, found the answer in another post:

In the coming release you will be able to make it use the alternate file manager as the default with a config setting

<add key="UseAlternateFileManagerAsDefault" value="true" />