To be brief, the lines are just reference points, and can't be relied on to be the end all for intonation. Without you playing a fretless much (assuming here, based on your question) it takes a long time to get your intonation good. Your ears and muscle memory are what will make you a good fretless player, not the lines. I honestly only use them when moving to second or third position, as a reference to a large hand movement. Once in place my ears are what I use for intonation, not the lines. When playing at the speed Jaco is, there is no time to look at the lines, and a note struck even a millimeter off will announce itself rather loudly, especially when doubling with another instrument. Anyone can play a fretted instrument fast, you really don't even have to be that accurate. The fretless is a whole other ball of wax.
I go from a fretless jazz to a fretted five string during my shows, and the concentration level needed to accurately play the fretless it at another level.
As an analogy, driving a car at 55 mph without cruise control would be playing fretless, where using cruise control would be a fretted bass.