I'm not a food chemist, but I think the answer to your questions is that any normal water you choose to use in a pizza dough will not have a level of acidity (low pH) that will adversely affect the fermentation process or the taste of a crust made from the dough--or your health. A pH of 5 is not high. A pH of 0 would be. Remember that acids are always being produced in a dough during fermentation as long as there is sufficient residual sugar to keep the fermentation process going. That process produces acidic by-products (carbonic, lactic, acetic, propionic, etc.) which are a major factor in lowering the pH in the dough. Doughs formed by using natural starters (e.g., sourdough starters) are loaded with acids--far higher than with normal doughs. Even at that, they are unlikely to ever approach a pH of 0 because of the buffering provided by the flour and other added ingredients. At the 0 level, if you could ever get there, I suspect the product would be so unpalatable as to be inedible.
Your water has a pH that is alkaline, and one way to lower the pH is to add an acid. White vinegar is one way of doing this. Using white vinegar in a baking product is fairly common, a good example of this being pie crust dough. Having done this myself, I could not detect the presence of the vinegar in the finished crust. Sometimes a bit of lemon juice, also an acidic product, is used in pie crust doughs.
The following excerpt, taken from a yeast website, might help explain this topic better than I:
The pH of doughs or preferments has little effect on yeast fermentation, unless it drops below 4.0. In general, data shows that yeast activity is fairly constant over a pH range of 4-6, which represents a 100-fold change in acidity. At the onset of fermentation, dough pH is approximately 5.5-5.8. However, during the course of fermentation, it decreases to 4.9-5.1, due to the production of carbonic acid (carbon-dioxide dissolved in water) and other organic acids. This pH drop is resisted by the buffering action of several dough ingredients. Both flour and milk are excellent buffers and help to maintain the pH range for optimum fermentation. Bakeries that use water brews add chemical buffers, such as calcium carbonate, to maintain a pH range of 4-6 during fermentation.
The reason why yeast is tolerant within the broad dough-pH range, is that the pH within the yeast cell remains quite constant at about 5.8, regardless of the pH variations in the dough. Since the various enzymes involved in yeast metabolism of sugars are located within the yeast cell, the gassing activity is relatively unaffected by external changes in pH."
The topic of dough pH is covered even more completely in this article: http://www.theartisan.net/The_Artisan_Yeast_Treatise_Section_Two.htm