If literal, "He is paying his dues, but sometimes late or cumulatively underpaying a little."
If figurative, "He has mostly earned his right to something through hard work or suffering." OR "He is now paying through hardship for some previously unearned good luck."
Need more context, but more or less it means to a varying or undetermined extent or degree. Yes, it can mean a plethora of things being that it's varying or undetermined.