Time management needs to be rewritten or simplified, and there also seems to be a bug with pondering.

The Ponder UCI option defaults to true, and AFAIK fishtest doesn't send ponder=off when running tests, and in Timemanager.cpp we have this:
if (Options["Ponder"])
optimumTime += optimumTime / 4;
Seems SF always uses 25% more time than originally intended.

Further, in TimeManager.h we have:
int available() const { return int(optimumTime * unstablePvFactor * 0.76); }

Currently we first add 25% time, and later remove 24%.