Most people are able to charge to 100%, even with degradation (or capacity loss). Sometimes a battery cannot charge to 100%, but then there is often actually a battery error (and then it gives a message saying battery cannot charge to 100% - you can search here for that error - it is associated with battery replacements).
Notification that battery cannot charge to 100%
That's correct, it is not useful for judging degradation. You cannot see degradation (let's call it capacity loss, not degradation) easily when using % (energy) display. The Energy Screen Trip Planner DOES take into account your degradation (it converts to available kWh and then converts back to arrival % for display).
I recommend tracking your number of rated miles at a given set %. To the extent that changes, that means you have less available energy above 0 rated miles. (You can extrapolate to 100% if you wish but it is not really necessary to charge to 100% unless your BMS has issues.)
Each rated mile typically corresponds to a particular amount of energy (different for different types of Model 3).
That being said, it IS still an estimate - but it's actually typically a very accurate estimate - inaccuracies in the estimate can least to extremely bad results (stranded!), so Tesla tries very hard to properly estimate available energy and display it on the screen.
The display of rated miles is a measure of that available energy - Take the available rated miles and multiply by the Wh/rmi (discharge) constant to give you your energy available (above 0 rated miles) at any point in time, as measured on the trip meter.
Constants for each Model 3