Your 3" rock layer will not prevent weed growth. Time will prove this. You are already having serious FA issues. With trout you have to be very careful using anything with copper as an active ingredient ESPECIALLY if your water has low alkalinity(hardness) less than 50mg/L. Trout are very sensitive to copper in softer water. Are the trout still eating pellets in the warm temperatures?
Have you measured the water temps at 7ft and the bottom?
Any well water inflow?
I see that Aquasphere from Healthy Ponds is a bacterial enzyme blend. Why are you not using it again?
Fathead minnows will not eat FA to any noticeable degree.
Removal of FA does remove accumulated nutrients. I have no idea how many pounds of FA that each 10 pounds of fish food grows. You will probably not ahead of nutrient accumulation but FA removal will help reduce it.
Blue pond dye will help reduce some FA growth in deeper water depending on darkness of the blue and type(brand) of dye.
For a noncopper algaecide control of FA, I would always first remove as much FA biomass as possible then I would try using Phycomycin or Green Clean Pro (peroxygen). It works best as hand spread granules when FA is small,short or in early growth on the bottom. Once the FA gets on top it is usually too advanced for peroxygen products unless a lot of material is used. Then you almost have to resort to using Cutrine Plus (copper product) liquid or granules depending on location and type of the algae. For trout ponds treat only small areas at a time 20-30 ft sections to minimize trout kills.
When fish are being fed daily it is hard to get effective FA control from bacterial and enzyme products. The best of these types of products will IMO come from AQUAFIX
www.naturalake.com They specialize in specialized bacterial and enzyme blends for specific types of problems. They also have a cold water active bacteria (Polar blend).
FA will be a constant problem in a pond water trout raising operation. One thing that will help reduce some FA is to not have too many trout in the pond - lower density results in less feeding and manure and FA.