Hi Bart,
I imagine Apple doesn't like myself, or anyone else saying so, but Font Book is not a very good font manager. Heck, even
their own PDF on the subject recommends using a third party app. Personally, I've been very happy with Suitcase X1. Others find FontAgent Pro to be a very stable manager, also. While I'm sure Font Book will continue to improve, you'd be much better off using a more mature font manager for now.
BUT... fonts you use in InDesign need to be in the /LIBRARY/APPLICATION SUPPORT/ADOBE/FONTS folder.
That is not correct. The fonts can be anywhere they are normally activated, or opened through a font manager. I never have any fonts in the folder you mention other than those in the Required folder. I use Suitcase X1 to control all of the fonts I want open or closed. The Adobe apps have no more problem seeing those fonts than any other program. The only advantage (if it can be said to be an advantage) to using that folder is that only the Adobe apps will see those fonts since they are the only apps that look in that folder. Otherwise, except for the required fonts, it has no special function or reason to exist. But yes, you are correct in saying ...
You can't use FontBook to get them back where they belong, so drag them into your Adobe fonts folder.
... since Font Book is a non functioning mess for Bart at the moment. At least he can continue on with his work in InDesign by using that workaround.