So it seems to be better there.
For some reason, it only scanned disks if the disk was handled by the trackdisk.device. Which today makes little sense as you probably want to install fonts from CD, a USB thumbdrive and so on...
It scans the RAD: disk but does not scan RAM: disk.
That's right. It only scans devices that have a "startup vector" and hence are usually handled by some sort of file system. RAM: does not fall into this scheme, even though it is a file system by its own. Why that decision was made is unclear to me. This is legacy code.
One other thing I noticed is if I do a manual source add to DF0: then it doesn't scan the 1st level directories. I have to go to the specific font dir. one by one.
That's correct. This is due to the format on which such "font add-on disks" where supposed to be delivered. You can read a bit more on this in the in-program help (press "HELP", then click on all the buttons - probably try the source button). There are two types of "font add-on disks" supported: The Amiga "font library disks", and so called PC "FAIS" disks. Foramts are a tiny bit different, and intellifont has scanning support for both of them. They had fonts in particular directories the program would find, and only such directories or places are scanned.
From the way how the code looks, I would say that this is essentially an Agfa program that was originally developped for PC, and then ported over to Amiga (with more or less success), taking the concepts of the PC workflow with it. The same also applies to the "bullet.library" which is actually an Agfa (compugraphic) library that was (rather poorly) ported to Amiga, and then, with lots of effort, fixed by Olaf.
For example, the bullet library in its original (3.1) incarnation was not even a proper library. Only one program could use it at a time. If more than two fonts were supposed to be created at the same time, they would both use the same global space in the library, overwriting each others data. As said, Olaf fixed this for 3.9, and it was a little polished for 3.1.4.