Actually, I just wanted to welcome you into the madness. Although I must admit that I have gotten better over the past 6 months since I got started, there are way much more questons than answers on my head at the moment. Eventually, the software grows on you, though...
I think the insertion of a tool stop is automatic and based on each operation you create. Whether you can disable this or not, I am not aware. I don't see why you would want to do it, though. Unless you had a gazillion operations with the exact same tool, but then I guess you can use Complex Machining and do all the passes at once. This is just a guess, though.
The Sprutcam Output generator is generating G Code output in either mils or mm's. Hence, all the driver computer does is execute the G Code. I don't think it can recalculate anything. I think you can add offsets and such, but that is pretty much it. Again, most likely based on a guess than on actual knowledge.
And one of the reasons I am willing to look like the ultimate fool is so that somebody with experience feels free to blow me out of the water. All I could do then is learn. Seems like a win-win situation to me!
And now to post my own question of doom... Good luck!