Hi Dave, what are you saying....fonts are damn interesting!!!
It was actually an interesting time for fonts for the Amiga, as it straddled the bitmap and vector style fonts era.
Some of this is going from memory, but the reason the apps would have their own fonts folder is speed and compatibility. The Amiga would slow down quite heavily when the Sys/fonts folder filled up, so if each app kept their fonts to their program folder, you could still have a zippy OS.
Of course the flip side is the other program could not use said fonts. I can't remember if font managers existed on the Amiga, I would be surprised if it didn't but that would allow you to activate and deactivate fonts in the Sys/fonts folder. So you had speed and variety.
The other issue is compatibility of fonts. PostScript(PS) especially, were very temperamental and had compatibility issues with different programs. Imagine 3D for example, uses PS fonts, but would not see the PS fonts Cinema 4D used.
I quite like the idea of keeping my system fonts folder lean and then if the software I use allows it, keep a separate folder for that app. with my massive CF cards on my system, space is not an issue.
I am busy doing the same as you, so I will post updates as I get on.