I can relate to your frustration, I'm an over-thinker myself, but I think you're being too hard on these instructors.
Their job is to: Keep you from killing yourself, teach you to fly, and teach you enough theory to pass the FAA test. That's it. If you need the science behind everything, more than what's in the FAA handbooks, you're going to need to accept that this is your thing, and learn it yourself. I'm not saying this to bust your chops, just to point out that a CFI's primary job isn't science teacher.
Flaps change the shape of the wing. They always increase drag, and in some cases they increase lift. So they can be used to help you reduce energy, to steepen an approach, and sometimes make a take-off shorter.
Before you add flaps, you need to make sure you're not above the max speed for deploying flaps, or you're liable to break something. Before you remove flaps, you need to make sure you have enough airspeed and potentially an appropriate angle of attack so you don't inadvertently stall the airplane.
On an engine failure, the number one thing, above anything else, is to make sure you don't stall the airplane. So the first thing you do is get the nose down, because whatever angle of attack you had under power, it's almost certainly not low enough for zero power. So engine out, nose down. Then, you want to get that speed to be best glide. Best glide is always a 'clean' speed. No flaps, gear up. Drag takes away energy, and with no engine your only energy source is your altitude. Best glide speed will get you the farthest distance with the altitude you have. So keep flying, get to V glide, fly to a place to land.
Once you are over the place you're going to land, or in the traffic pattern, you can think about adding drag to the airplane. This is where some personal preferences can come in to play. If I'm over an airport, I plan on landing about 1/3 of the way down the field, even if it's a short field. I believe that's FAA recommendations, and I like it because it gives me a margin for error in not being short. I would much rather be too high, and risk going too long, than going short. The next thing I do is err on the side of being too high, at each step. So if I'm doing a circle to land, and I'm coming out way above normal pattern, but I'm not 100% positive I can't easily make another turn, I'm not doing it. Along those lines, I don't add any flaps on a simulated power out until I'm on final. That may not be the best way to do it, but I'm more comfortable with my ability to lose altitude than add energy to an aircraft without an operating engine.
One final thought on an already long post. If you're high on final, other than adding flaps or slipping, slowing down will increase your descent rate. Obviously don't stall or even increase AOA to a point where you could get too slow too quickly, but as you're already below best glide, slower is steeper. In calm weather, being at about 1.1 V stall on a straight in final isn't necessarily bad. Likewise, if you're a little too low, you can get back up to V glide to lengthen your glide. I don't find myself in that spot on simulated, because I get out of best glide while I'm still high. If it's simulated, you're at best glide already, and you know you're not going to make the field, add power, go-around, and try again. No point in starting the go-around low if you don't have to.
