You can't limit algae growth by keeping the nutrients at a low level in the water. Algae require very small amount of nutrients compared to aquatic plants. Just look at how tiny the mass of algae is even when you have a big algae bloom in the tank. That small mass means it didn't take much of any nutrients to build it. By contrast, aquatic plants can build up a significant mass, using the nutrients to build it.
When you limit your fertilizing to substrate fertilizing, you still can't keep those nutrients out of the water. All of the nutrients are in the form of ions, portions of salts. The salts in the substrate will migrate to the water, because areas of high concentration always contribute the salts to the water that is in contact. And, the water in the substrate is certainly in contact with the tank water.
It isn't just the mass of plants that inhibits algae growth, it is the mass of healthy plants growing as fast as the light lets them grow. I have no idea how this happens, but tanks filled with healthy plants that are not limited in growth by anything except light, will rarely have algae problems. Once you limit the growth of the plants by reducing their access to the nutrients they need, algae will always follow. Maybe it is magic??