A. If you use the metronome to keep you in time, I submit you don't really know the part. YOU have to keep time, not rely on the 'nome or the drums. Practice slow and precise, it's OK to play out of time as you work out fingering , etc.
B. To work on ensuring you are playing in time, set the 'nome to only click on 2 and 4 ( or set a drum machine to only give you snare hits on 2 and 4). This makes YOU provide 1 and 3, one of the fundamental aspects of your job. Can't play with only 2 and 4, but can with a full drum track? Means you ain't keeping time, you're riding someone else's time.
C. Absolutely one can improve their ability to articulate music in time. Just as one can learn to recognize intervals by practicing with a fixed reference, one can learn to keep time by working with a fixed reference. But you have to listen to yourself and stand alone. That's the reason for only using the reference for part of the measure.
John