Certain encounters are not marked on the map.
Lower Caves:
Abandoned Waterway facility Western area (xpbl_ojyc3) - coil spider (present as a picture but is not in the list), cave ears
Abandoned Waterway facility Eastern area (xpbl_ojyc1) - gremlin stool, red dream mushroom, oozing shroom
Silent Isle (si1) - rathound, psi beetle, mindshroom, mysterious pillars
Chancer's Bay (cvw5) - lake poppy
Junkyard (Depot B) - mindshroom
Old Ib's Homestead (cvw18x) - cave hopper
Core Ring (cvw27) - red dream mushroom
Core Ring (cvw11) - mindshroom
Caves (cvw17x) - coil spider, cave ears
Rig Periphery (cvw9) - cave ears
Hunting Grounds (cvw_hg2) - cave ears
Upper Caves:
lux-a5 - cave hopper
lux-a6x - cave ears
lux-b8 - lake poppy
Deep Caverns:
Rathound Lair (dc_rh) - spirit mushroom
Black Sea:
Fetid Marsh (xpbl_k4) - lingula
Fetid Marsh (xpbl_k6) - lingula, green wart, honey stalks
Fetid Marsh (xpbl_l5) - lingula, glittershroom
Basalt Cave (xpbl_l7) - honey stalks
Siphoner pools (xpbl_siph1) - lingula, green wart
xpbl_f9 - lingula
Would be reasonable to remove unreachable plants or fungi from the list (or make them non-interactive):
cv9 - unreachable lake poppy
cv11 - unreachable mindshroom (maybe add agility check to jump there)
Chancer's Bay (cvw5) - unreachable mindshroom