#1 It always works for me as expected when I use Smart Dimension. Make sure you are selecting the edge of the hole (at appox 45 degrees).
#2 These are Hole Wizzard Model Items. You can turn them off here... Just uncheck With thread callout (Tapped hole example)
#3 These are center marks and you can control them here...(Insert>Annotations>Center Mark) Uncheck Auto Insert boxes.
1. I'm having trouble picturing the issue without seeing a screenshot, but if the dimension is coming in at 90° then you're selecting perpendicular edges.
2. I believe Rick Becker answered that one.
3. You may need to de-select this option.
#1 Make sure you select the center mark line that is parallel to the edge you are dimensioning to. Sometimes you may have to zoom in order to make sure you select that specific center mark line. I run into this often.
I make it a habit to never select the centerlines. I want my dimensions to be to the hole itself. I have had dangling centerlines and I have found that dimensioning to them scary.