Yes, Seiryu stone alters water parameters. I have some in my tank, but they are small stones that were sold for a nano tank ( I have a 40 breeder) so they haven't caused problems. Since you knew these stones were causing a problem, why did you keep them? Keeping for the sake of not having to dose calcium while they are reeking havoc on the rest of your water parameters is not a good idea. It is easy enough to remineralize RO water and for a small tank, it will cost next to nothing to do so. Planted tanks like stability.
As for the green spot algae, this isn't always a phosphate problem. If you have high organics in your tank from dying plants, that too can cause green spot.
While it is true that plants melt and go through awkward phases as they adjust to new environment, sick plants are algae magnets. Mosses in general tend to be algae magnets because they collect stuff that is floating around in the water column. Vacuuming them or using a soft toothbrush to remove the detritus they collect once a week during a water change keeps them algae free. Some mosses also need to be trimmed as the base layer will die off without light which causes more problems with organics in the water column.
What does your tank maintenance schedule look like?
As for EI itself, I'm not willing to go into that rabbithole, but I will say that it is meant to be modified. My bottle of orange water from Tropica is also EI, but it doesn't contain nitrates or phosphorus. I don't dose my tank what Tropica recommends as I don't use CO2, I don't have stems to feed and my fast growers Vals and Giant Hairgrass are given root tabs which contains some phosphates, but most of the phosphates in my tank comes from fish food.
There is no true definition of 'heavily planted', but usually that means more than 75% of a persons' tank is covered with plant mass. Your tank does not meet that so-called standard.