In my opinion it takes 5000 miles of seat time and then will truly feel comfortable, safe and "at home" with a particular motorcycle.
I am just beginning to experience that feeling now at 2500 miles. if you read some of my earliest posts on this forum I commented that i felt as timid as a street cat during my first month of ownership and would toot the horn at every car that had its nose sticking out to pull onto the street. I felt like every car was about to crash into me or did not see me.
Fast forward 6 months later and the "close calls" are very few and far between. I really like and recommend the book "Proficient Motorcycling", that is a fantastic read.
2016 CB300F - 6200 miles - 100% stock config