Your understanding of mechanics is off base. By this logic, running any pace slower than your race pace would be harmful because it "adapt(s) you to running with your calves overextended and a low cadence".
Extra range of motion means EXACTLY that a muscle is working harder. If your foot is a lever and your ankle is the fulcrum, your body weight is the resistance. Moving the lever (your foot and ankle) through a longer range of motion means you are doing more work. Work being force times distance, the force is your body weight which is constant, and the distance is increased since you are climbing.
As for recruiting "extra muscle fibers on hills", that can only be a good thing. Your muscle is an organ. Let's take the gastrocnemius (calf) as an example since we're talking about it. When you're running, uphill or downhill or flat, you are contracting the gastroc (among other things) to propel you forward. The nerves that send the signals to your gastroc telling it to fire (in a complex called motor units) send a signal that tells first your Type I fibers, then your Type IIA fibers, and finally your Type IIX (or IIB, whatever your naming standard is) to fire. Given the speeds that we're talking about, you are realistically activating all of those on both flat and uphill. There are no extra fibers recruited to increase range of motion, they simply contract through more positions, in this case through a larger angle because your foot will be dorsiflexed (toes pointed up) while running uphill. Starting your contractions from that more dorsiflexed position (as opposed to running flat) will both make you work harder (stated above) and increase your strength through that range of motion. Muscles adapt to get stronger only though the range of motions you use them in.
This is easily equatable to an issue in resistance training. Picture yourself bench pressing. Good Strength and Conditioning Coaches will always tell you to go through the full range of motion when doing this exercise. When you see someone lower a weight most of the way down, but not all the way to the chest, they are not getting the full benefit of that exercise. If you do this consistently, you are losing those few degrees at the bottom of your lift and you will be significantly weaker in that position. If you can bench 200 pounds in your less than full ROM, but attempt to bench maybe 185 going through full ROM (bar to chest) you may find that you can't lift the weight because you're weak in that bar-to-chest area. It's commonly known as a "sticking point".
Does that mean you can't bench 200lbs, or more applicably, that you can't run as fast? No, not necessarily. But you will always be more prepared and better adapted through that increased ROM. I wouldn't sacrifice any true, late season speed work for increased hill repeats, but I will still be running hill repeats, thank you very much.