elcruxio

Toe clips tend to have the foot further back from the pedal axle than clipless and that's a big factor for saddle height.

Now I don't actually use the 103 %, because formulae are stupid. For whatever reason you latched on to that number. But it does apparently give peak power so whatever. I'm at 102% I think, but that's with shoes off. Wasn't a figure I was aiming for but rather I checked it out of curiosity.
Actually it's kinda complicated since I use three pairs of shoes and they all have wildly varying sole thicknesses. And come to think of it the cleat fore aft might be different too since I've just pushed the cleats as far back as they can go.

Letting the joint unload at the bottom of the stroke just seems like a recipe for pain.

Firstly the loaded joint and the whole leg serves a purpose. After the main power stroke the bottom leg needs to support the rider UNTIL the upper leg travels over the peak and begins its own power stroke. If your bottom leg isn't supporting the rider you'll experience pelvic instability, which in turn causes hip pain, saddle sores, numb genitals, back pain, shoulder and neck pain, arm pain, hand pain, hand numbness etc. Some of those are caused by compensating btw.

Secondly (analogies are also kinda stupid in this context but I'll give it a shot anyway), If you unload so much as to let the muscles around the joint relax It's kinda like throwing a ball and letting the arm go completely slack at the follow through. That'll jolt and rip the muscles and tendons and after a while it'll start breaking stuff. If your saddle is too high, that same thing will happen at the knee albeit at a lesser rate. If the saddle is high enough to allow for unloading the leg there's this observable acceleration of the knee joint at the bottom of the stroke and that really isn't good for you long term. Even if the effect is slight, there's so many repetitions that over time it's going to start taking a toll.

I believe the general agreement is that riders should have their knee flexion at 25-35 degrees at the bottom of the stroke. The 109 % formula leaves over half of riders and closer to two thirds outside that value. Since the 109 % is a pretty high saddle height to begin with that'll almost automatically mean that almost two thirds of riders setup with the 109 % end up with a smaller than 25 degree knee flexion at the bottom of the pedal stroke. You'll need some freaky mobility to be able to pull that off with an intact pedal stroke. I suspect that riders who fell within the specified range had their cleats quite far forward on the shoe.

Personally I feel that aiming for 25 - 35 degrees knee flexion is a bit tricky as people'll try to achieve middle of those values when many riders would function better near the 35 degrees, especially if you work sitting down. But of course even degrees are stupid in isolation as they do not account for mobility, cleat position, pedal stroke, ankle flexion, or how the rider is feeling.