There is a setting "Additional fonts with font substitution" in Text Area option pane, off by default. When the user ticks the box, 2 other controls appear: listbox of fonts and a checkbox "Font substitution: Search all system fonts". So the checkbox labelled "Additional fonts..." actually works as a checkbox "Font substitution", but has a misleading name.
If I am to turn on the font substitution I look for "Font substition" checkbox, but there is no such checkbox.
Another problem from this non user friendly interface: If I have both checkboxes on ("Additional..." and "...system fonts") I may want to untick "Additional". And what happens? All font substitution controls disappear making me wondering if "...system fonts" will still be honored or not.
How to improve it? Just add this intuitive "Font substitution" checkbox which will enable 3 controls mentioned above. Do not use "Additional fonts..." checkbox as a multifunctional secret passage.
using jedit trunk (21796 2012-06-11), win 7 64, sun java 6.