Alright…I think I figured out what’s going on. The penalty count only seems to show up when the user is at trust level 2…and, I suspect, only if the suspension is allowed to time out. If you manually lift the suspension, the counter doesn’t increment, so there’s nothing to clear.
The counter itself is glitchy, though. If you manually unsuspend the user, it doesn’t increment, but it also doesn’t show as a “removed suspension” in the log. Furthermore, I tested this by manually suspending, then unsuspending a user several times before clearing the penalty count on the third or fourth suspension. That retroactively marked all of the previous suspensions on my test account as “removed” and ended up giving my account a negative penalty count.
Note that this also made the account ineligible for trust level upgrade:
So it looks like while what my initial question addressed might be expected behavior, there may still be some glitches in the counting mechanism.