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Golux, I think the difference is that a starting battery in being asked to put out about one or one and a half kilowatt (for engines up to "car" size) for about 3-5 seconds, no more. With a bow thruster you may be wanting to use it for more than 3-5 seconds. That puts you into deep cycle territory.
You also don't have to run monster cables up front, if there's a deep cycle battery up front. The battery can run the thruster, and the thinner cables will just recharge it a bit slower. Compromises.
Dave, I think the devil will lie in the details, as usual. If a single Group31 battery (large car battery) can suply 3500A into a dead short, it can certainly supply the kilowatt to run a starter motor for a few seconds without being drawn down much. A 50-100A load for four seconds still represents a tiny fraction of what the battery has stored--if you have a sufficiently large battery/bank. It's kind of like saying fleas can kill a dog by sucking all of its blood. Well, yes, they can. But one bite once a day, won't be intolerable much less fatal.
Carrying a totally isolated separate starting battery? Great if you can afford the dedicated inflexible resource, and the space and weight penalty, I guess. Since the engineering behind batteries hasn't really changed in the past decades, I have to wonder why "the norm" and the recommendations have shifted over the last 20-40 years, from having an A/B setup to having one house and one starting. Style, more than science, perhaps?