"Cut-Throughs along the far left edge may break cutting bits due to the board leaving the aux roller"
The "aux rollers" are the two long rollers that run over the top of the board. If your board comes out from under one of the rollers, it could tip up, breaking the bit. By having either a "real" board that is 7" inches longer than your virtual board or in a jig, you can ignore the message.
If you get the message that the top edge will not cut through, it is due to protecting the brass roller. Either keep your cuts 1/2 inch from the top edge or place in a sled.
Hope that helps