In prototypes/content/gold/tiles.lua (lines 18-24), natural-gold-soil has two prototype misconfigurations (likely remnants copied from Vulcanus tiles):

layer = 85,
searchable = true,
transitions = lava_stone_transitions,
transitions_between_transitions = data.raw["tile"]["landfill"].transitions_between_transitions,

1. transitions = lava_stone_transitions: In vanilla Space Age, lava_stone_transitions is a local variable in tiles-vulcanus.lua, so in Lignumis it evaluates to nil.
2. layer = 85 and transitions_between_transitions = landfill: Layer 85 is unusually high for natural ground on Nauvis (vanilla Nauvis ground is normally 10-33). Borrowing landfill transitions causes pitch-black rectangular graphical glitches along the border when adjacent to certain modded tiles (e.g. tiles with custom transition groups or lightmaps).

Suggested fix:

layer = 25,
searchable = true,
transitions = data.raw["tile"]["dirt-1"].transitions,
transitions_between_transitions = data.raw["tile"]["dirt-1"].transitions_between_transitions,

I don't really see a change but sure :-)

Yes, only
at planet-crucible: (https://mods.factorio.com/mod/planet-crucible/discussion/6ae452a1fb5eea50494d9119)
it causes this problem in your mod.
I temporarily fixed planet-crucible, but found that the problem still exists. I could only solve the texture error by modifying both planet-crucible and lignumis at the same time, so that's why I'm reporting this to you—as a double safeguard.