With a Prius you don't even have to vary your speed to have the engine speed vary. Unless you are driving on an absolutely flat plain! The engine speed varies as you go up and down even the smallest hills, so small you don't even notice them. As far as brakes, being careful with new brakes is nothing new. The problem is the pads haven't yet warn down so the full surface is contacting the rotor and/or drum. This means all necessary braking force could be concentrated on smaller areas of the rotor or drum. This can heat the rotor or drum unevenly, which can result in warping or burning of the metal. So for a while you drive gently to wear the pads in. It doesn't take long. Some even apply the brakes while driving to wear them in more quickly. Being careful, of course, not to heat them up too much.
While this is somewhat true I urge caution in the generalization. Small rises and falls will tend to NOT vary the ICE rpm at all, but rather the battery will fluctuate flow to carry over a rise or regen during a fall. Now, what a significant rise or fall is will vary, but on a long highway or interstate drive I'll tell you that the ICE rpm will not vary very much in most parts of our interstate highway system. Now, whether that really matters a lick I'm skeptical of, I think that you could drop into the driver's seat of a brand new Prius, drive a steady 65mph on a perfectly flat road for the first 1000 miles and do absolutely no harm at all...but nobody wants to take the chance of being wrong with their shiny new baby either! In any case, there are a lot of reasons to take the back roads, and if one of them happens to be that it might help break-in, then all the better.