Pizza Tower is a similar game that utilizes combo's well. Rewarding speed while not punishing exploration. Outside of the escape sections that start around the latter half of the levels, players can just explore and go as slow as they want, but a combo meter in the upper right of the screen will reward players who can chain actions together. Various actions may extend the combo timer more than others, like beating an enemy resets it fully while picking up a single score item (though often grouped together) will just push it back a little.

Another example is Rayman 3. While generally a slower paced 3D action/platformer, there's this combo based score system that rewards chaining actions together, with (again) beating enemies extending the combo timer for longer than picking up items. Making a longer chain also increases the multiplier, so it helps to strategize and pickup higher valued items later in the chain. We used to try and optimize for the best score as a community effort way back, and it was fun to find ways to make combo's the developers never intended, even overflowing the score counter. Felt like beating the house, lol.

All in all, I do prefer combo systems over timers when it comes to rewarding speed in games.