1. The "Bonus" columns in the D1,2,3 lines don't actually show a bonus, but an allowable datum shift. There is a difference between those things.
2. The only true bonus is for the tolerated element itself. In this case it's an OD, the MMC bonus is Upper Limit Diameter (MMC of an OD) minus Actual Diameter, giving 0,0050.
3. Your actual deviation is 0,0035. No need for the bonus to kick in, let alone the datum shift. That will only happen when your actual is OOT, so your tube position made it in tolerance all on its own. Congratulations!