My Swan machine has lines on the track but I never use them. I set the depth gauge every time I use it, based on the actual position of the bit in the chuck. Sometimes the bit is higher or lower in the chuck and can't be certain that it aligns with the marks on the track.
After I chuck up a bit, which could be a different length than another bit, I set the bit down onto the timber with the lead screw hanging over the side of the timber. And with the "wing" of the bit on the top of the timber, this position is zero. Measuring down the track from the bottom of the carriage, I set my depth gauge, using a wooden folding ruler.
I never bore all the way through a timber when creating a mortise. Such as a tie beam through mortise. I bore half way from each side.
The only time I bore all the way down to the bottom of the timber is when I'm boring a peg hole. However, I don't bore through the bottom of the timber surface. I stop when the bit lead screw pokes through.
And I finish off the peg hole with a bit and brace of the same size.
Watch the end of this video to see this procedure:
Jim Rogers