I can’t speak for all of them, but ForeFlight certainly does the fuel and altitude and speed calculations and I adjust for best altitude (takes seconds). I believe the few times I used Fltplan.com it did too. As far as enroute wind differences, yes, you get real time correction. You can also download the most recent forecasts right before takeoff (with instant results) and there are other tools for collecting weather data enroute, such as ADSB an XM). Maybe better training with modern tools would help with these misunderstandings.