Step 1: Have you calibrated your NO3 test?
I would not over dose, but increase your dosing just a bit, then monitor it for a week or two, (3-4 water changes) and see if it is trending upwards, and where it starts to level off. Perhaps increase your dosing by 25% (dose one more time per week, or a little more each time you do dose)
I have done something close to 100% water changes on some tanks (oops- sorry fish, they were almost stranded) and refilled with tap water. My tap water shows 1 ppm chlorine and 1 ppm ammonia from chloramine. Prime and similar products (I have used Chloramine Buster a lot) work just fine as a dechlor.
Think of it this way:
Before you did the water change the water had some ammonia from the fish and from decomposing things in there. The bacteria is used to dealing with that, and can handle that much ammonia spread out over the course of the day so you cannot tell there is any ammonia present.
When you do a water change you are removing whatever ammonia is in the water and replacing it with ammonia from the tap water. So the bacteria get to work on this. The Prime keeps it from being toxic, and before the Prime is deactivated the bacteria have handled all the ammonia.
The plants also take in ammonia- most aquatic plants prefer ammonia over nitrate or nitrite as their source of nitrogen.
If you do 2 water changes back to back with that small a storage source it is not a whole lot better. However, if this method is working for you, keep on going with it. Use those small water changes to vacuum the tank almost every time, and clean the filter media as needed. But really look into a larger prep method. Some disaster could happen that can best be solved with a much larger water change, and being able to have more water ready to use can make the difference. Perhaps think about prepping RO in the barrel (no GH booster) and matching it with tap water (which supplies excess GH) with the net result that you could possibly do a 50% water change in case of emergency.