I have done several tests but I am still struggling with basic configuration of FOP.
As Adam mentioned here it seems FOP somehow ignores <font-base/> and even <base/> if the config is provided to FOP dynamically from XQuery.
If I use FOP 2.1 on command line, everything works, no matter if I use full path to a filesystem or some url (e.g. to a rest point of an eXist app). Hence I guess this problem lies somewhere between eXist and FOP.
It is possible to use workaround and load fronts from the filesystem directly with @embed-url: <font kerning="yes" embed-url="file://full-path-to-fonts-in-expathrepo/libertine/font.ttf" embedding-mode="subset">
If I try to use <font-base/> with exactly the same path, it does not work:
Tests with eXist 3.0 stable are done on Ubuntu 12.04 LTS, tests with FOP 2.1 are done on Ubuntu 16.04 LTS. I am doing that because in 12.04 version it is not easy to upgrade to FOP 2.1. Later I want to migrate eXist there too.