You make a valid observation but I think it gets a bit more complicated than the salt/water relationship alone. If other ingredients are added to the dough, such as sugar, oil, or vital wheat gluten, or whatever, the same scientific principles apply. I know that you personally may not be concerned about sugar, oil, etc., in the doughs you have been making but some members who are trying to make Neapolitan-style pizzas in their home ovens frequently use sugar and/or oil in their doughs. When Marco first posted a basic Neapolitan dough recipe on the forum, I naturally assumed that all of the ingredients (other than flour) were based on a percentage of the flour. This included the Crescito. Somewhere along the way, I was promptly corrected by Marco and told that the 1-5% Crescito figure was in relation to the water. Even with that, I assumed that the salt, at 45 grams, was in relation to the flour (1650 grams), not water, and have proceeded on that assumption ever since. Otherwise, 45 grams in relation to a liter of water (1000 grams) would be 4.5%--on the surface a seemingly excessive amount of salt. On the basis of the flour (1650 grams), it would be 2.73%, which is a number that is more in line with what most people consider to be a proper number for salt.
Most spreadsheets work along the lines that Bill has discussed, and as Jack has commented. There is a fixed dough weight and if one number is changed, such as percent hydration, the percents of the other numbers do not change. If other percents are changed for other ingredients, the ingredient quantities will change individually but the total dough ball weight will remain the same, principles of chemistry notwithstanding. I have designed a new preferment dough calculating tool with Boy Hits Car (Mike) that works the same way as most spreadsheets. In due course, I expect the tool to be posted on the forum. Because of the many ways that people use their preferments (which includes starters used solely for leavening purposes), we designed the tool so that the preferment can be expressed in any one of the three ways you referenced in your post, including expressing the amount of preferment as a percentage of water. To test the tool, I converted one of Bill's dough formulations to the three different methods, and the results were the same. So as long as the numbers are correct, it doesn't matter how one expresses the preferment. The tool also allows one to include sugar and/or oil, mainly for the benefit of those using standard home ovens. Users also have the option of supplementing their natural (wild yeast) preferments with commercial yeast, as part of the final mix, as is commonly done with many of our members. Yet, the ingredients like salt, yeast, sugar and oil remain fixed from a percentage standpoint.