Realistically, I don't think it'll be possible to have a 100% accurate profile due to external factors like wind. In my opinion 1t is close enough that it can be disregarded. You can play with the fuel factor on simbrief if it is not accurate enough for you.
Definitely seems to be a Navdata issue as the default VFR map also shows those runways. Nothing we can do there unfortunately. And yes, currently we don't use Navigraph, we are working on implementing it though.
You wouldn't change the wheels when they are only "yellow" in the real world.
But more likely then not it is down to the specific airline anyways and you wont really find a setting that pleases everyone 😅
Testing this again just now, it doesn't seem to be working 100%, at least the Selcal one. So will take another look at it.
You'll need to enable this option in the menu for it to work though.