I'll put my ideas here in case others are interested. At a glance, I see two ways to handle navigation in this module that should be doable in a trifold format but maybe with some design challenges/compromises elsewhere.
1. Normal-ish point crawl with hinting and repeated locations
Just give the Warden a straightforward "numbered circles with lines connecting them" map, but use narrative cues to make sure the players know where the unique locations are, roughly speaking (e.g. the other factions' camps might be sighted from a hilltop, or during the crash landing). It's then up to them if they visit. If some of the planet-based locations are particularly important, they can appear in multiple places. E.g. all the outermost regular nodes could have open branches going outward and the module could say if they venture past that point in any direction they'll encounter a Simulacrum Garden.
If you put the duplicates far apart, it's somewhat unlikely that the players will visit multiples, and the Warden can vary the repeats if they do. E.g. the second occurrence of Cerulean Falls might not have a waterfall, but just a pool with a now-familiar-looking structure at the bottom.
2. Randomized map plus linear "Plot Locations"
Keep your current locations as the "Plot Locations" that will be encountered in fixed order, but don't tell the players that. Direct the Warden to have the players keep a map, or keep one for them. They start at the ship and each time they travel for an hour, you roll on a table. Something like:
1-4 Various single-line prompts that the Warden can just use as scenery they're passing through or possibly short encounters if the players engage.
5-6 Common hazards like bogs or tangled growth that make the node take twice as long to cross.
7-8 The players catch sight of the next Plot Location at an adjacent node (or otherwise receive clues about its existence, like tracks to follow), and can choose whether to head towards it or change direction to avoid it. Place it on the map whether or not they go there.
9-10 The players stumble across the next Plot Location. Place it in their current node and begin the encounter immediately.
The nodes and connections could be placed organically with boxes and lines, or you could be building a square- or hex-grid map as you go. But either way, you still get the players everywhere they need to go, but the relative positioning of all the locations depends on how they go about exploring, and might present shortcuts between the locations at later stages.
Additional rolls of 6-10 once all the Plot Locations are on the map could trigger attacks or advance the clock faster, to hasten the endgame if the players are wasting too much time wandering around.