In general the site is considered conservative. I would say its a guide to use "on paper" before you start observing your real aquarium with real fish. It will usually prevent you overstocking a tank, it will give you an idea of how much water to change. It will you give you a clue to the temperament and compatibility of different fish species and what people generally find works or dont work. Add new fish gradually, test the water, observe the fish, determine your stocking and water change routine.
It cant make allowances for anything you didnt input. For instance your tap water may be treated with chloramine rather than chlorine, or your tap water may contain nitrate in which case your water changes wont be effective as they would if the new water was clear of these nitrogen impurities and you should change more water or stock more lightly or both. It cant take account of how much food you put in the tank. It cant take account of plants in the tank which will help with water quality. Your aquascape reduces water volume. It cant take account of the personalities of specific individual fish. Its all a bit of a generalisation and makes assumptions so it can be a functional website.
The sites calculations for stock levels and water change routine are probably based on nitrate build up, and nobody knows what they are using as a safe upper limit. From experience of using the site and observing my own aquariums water quality, I presume they are working to about 20ppm as an upper limit for the freshwater side of the site. Some people are happy to push that out to 40ppm and stock more heavily and/ or change water less frequently. Some people feel that 20ppm is too high and work to 10ppm or even 5ppm and stock more cautiously and/ or change water more often. You have to decide for yourself on matters like these.
if you are planning on changing 30% of the water, may as well take an extra 5 minutes and change 50%. If 50% weekly keeps you below whatever water quality target you have set yourself and you feel a few more fish wont disrupt the interactions with your fish, then add a few more if thats your wish. If 50% weekly water changes arent keeping you below your water quality target you either have to accept poorer water quality or reduce the fish.