It is all in the orientation of the filter. The glass bowl which has the in and out side at the same height it should be full as fuel comes in, goes to the bottom and then back out the top. The inline depends on its orientation - if you had it mounted vertically with in at the bottom then the filter will fill up before fuel can get out to top so would be full all the time. Mine is on its side so the filter only ever half fills as fuel is going out to the engine as fast as it goes in from the pump.
The carb floats allow the right amount of fuel in and as long as the fuel is in the filter so it can get out the outlet then the the engine gets all the fuel it needs.
"Assuming they don't "need" to be full, how does the engine "know" how much fuel needs to be / should be in the filter bowls?" The engine does not need to know other than the fuel pump providing the the right amount of fuel at the right pressure
Julian - try not to over think these things
Garry