You can add system water to give them the nutrients.

I'm not sure what you mean by adding regular pH water. The 5.5 pH is for soaking the cubes to remove the leftover lime from the manufacturing process. Plants do prefer soils with a lower pH usually in the 5 to 6 range and this has to do with nutrient availability.

Seedlings, just like "normal" adult plants need nutrients to grow. If you are only feeding your plants pure water, they will definitely suffer if not die altogether.