I'm fairly sure Chartist vessels use the same sorts of engines as mainline Imperial ships. The primary difference is that Chartist ships generally don't have navigators. And without one, you're restricted to the very well known routes that are reasonably constant, and don't dare risk anything more variable. A Navigator can make course corrections if the Warp is threatening to shift you away from your intended destination, and can generally operate with just some decent guidelines as to their destination, rather than a fixed route.

This, incidentally, is the reasoning behind the Navigator Houses. If you want to make a long journey, or one into less calm regions of space, you need a Navigator. Machines just can't handle the ridiculously convoluted moves needed to steer in the warp (or rather, they can't without being possessed by daemons), and that means the Navigators effectively have a monopoly on interstellar travel. The Emperor established multiple Houses with distinct bloodlines both as a means of ensuring quality (so one flaw couldn't take them all out) and as a means to keep the Navigators from basically owning the Imperium.

Incidentally, I'd argue that widespread and reliable access to Navigator-like individuals is what allows a species in the 40k galaxy to count as a galactic power. The Imperium has it's Navigators, Chaos has it's sorcerers and/or daemon hosts, Orks have their Weirdboyz, and the Tyranids have a sort of gestalt mind that works in much the same overall way. The Eldar and Necrons essentially cheat by avoiding the Warp altogether. There are quite literally thousands of other species out there, but without Navigators, none of them are ever going to be able to content with the super-powers on any meaningful strategic level.

The Culture, from what I've seen, also fall into the 'cheats' category. But they should be aware of the sheer anarchy that will follow if they let their technology become more widely available.