Sprut has a 6th sense and with all the room in the world it will still be line right over any fastener.
There is a couple ways to control this
1) operation parameters - transition tab- short link distance to a value above your fasteners or safe level if there is a stepover type option then set this to via safe plane also.
2) operation parameters - parameters tab -z retract height set to value above your fasteners or safe level.
both of these are important to set for most types of operations
hope this helps
Found a clip I had loaded
I tend to review each operation and look for collisions or problems. I found sput will show all the paths and you can see a low or problem one.
Even If you don't use fixtures to visualize and verify clearance you can still estimate and or see a low transition move
Note red dotted lines, I use these views to check for problems