They can be. And in fact, in plenty of electronic devices they are since operating from a variable supply voltage is not an option so the typical battery powered device uses dc-dc converter like the one in the article only it does not operate on a single cell but on all cells in series. And that works just fine.

> But in my remote, the batteries are not arranged in serial; they are arranged in parallel

Are you sure? That's pretty uncommon. Are the poles oriented in the same direction or opposite ones? Is one set of poles connected to a pair of terminals shared by a single conductor and the other set using two distinct terminals?