Consider a game in which each move must be made within 8 ns of real time. Two identical engines will play, sharing a single core. With pondering disabled, engine A gets 8 ns of CPU time and makes a move, engine B gets 8 ns of CPU time and makes a move, etc. Each move is the result of 8 ns of computation.
With pondering enabled, on the very first move engine A has only had access to the CPU for 4 ns before 8 ns of real time expires. During this time, engine B has had 4 ns of pondering. When engine A makes its move, engine B realizes that most of its pondering was based on an incorrect guess of the move that engine A would make. Suppose that only 25% of engine B's pondering was applicable. Of the 4 ns that engine B spent pondering, only 1 ns was actually useful.
Now it's engine B's turn. Like engine A, engine B only gets access to the CPU for 4 ns before 8 ns of real time expires. Counting the 1 ns of useful pondering, engine B has applied 5 ns of CPU time to its move. During this time engine A has had 4 ns of pondering, but again, only 25% (1 ns) is useful. On engine A's next turn it will also have applied 5 ns of CPU time to its move. With pondering, each move is the result of 5 ns of computation, except for the very first move, which is the result of only 4 ns of computation. You will get a better game (both engines performing more calculations per move) if you disable pondering.
If the engines are different the results will depend on engine implementation. In the extreme case, imagine that engine A can compute the absolutely best move with exactly 8 ns of computation, but after 4 ns it has only a wild guess. Engine B's performance scales much smoother with the amount of time it has to think. In this silly example, with pondering disabled engine A will win every game, but with pondering enabled engine B will win every game. I suspect that in real life, between two real engines, pondering will decrease the quality of the game fairly evenly, without giving either engine an advantage.
If the per-move time restriction is replaced with a total time restriction I think the results would be similar, except that the way in which engines decide how much time to commit to a move would have a greater effect. That is, I think that pondering would amplify the importance of deciding whether a move requires additional thinking time.
Taking all that together: if you want a battle between engines performing at their peak but you only have one core, disable pondering.