Any tool is only as good as the person using it.
I use that BMR calculator and my HR monitor to estimate my daily caloric needs, and it agrees well with changes on the scale.
What I do is take the lower of the two methods for estimating BMR and multiply that number by 1.2 to account for my desk job (multiply your BMR by 1.4 if you have an active job). Then I add in what my HR monitor estimated for calories burned during exercise, and eat that amount. If I want to lose weight I subtract 500 from that number.
E.g. on an easy day it might look like this (1650 x 1.2) + 800 – 500 = 2280kcal.
Sure a whole bunch of estimates are used, but any errors pretty much cancel.