As you say the tolerances are very tight (functZeroLevelDefault => 1E-14, functZeroLevelTolDefault => 1E-12) and are the same as the analogous numerical tolerances. These are probably exactly what Mike and I first set when we wrote the function compare algorithm back in 1996 or so. And the defaults (which are set in global.conf) were just based on an educated (but not a very educated) guess.
If you have some experience from looking at examples what might be more reasonable values to use, it would probably be good to change these.
Arnie