Hmm, everyone will probably have very different opinions on that, but here are my rough thoughts:
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using an uncertainty value would take some fiddling to get it right, otherwise someone could just take the central value and be very close to the initial observation. Personally I don’t mind if the observation on the map is within a bounding/obscuring box without the observation location or coordinate actually showing (or being randomly shifted within that box), as long as the observation is still listed (with obscured coordinates) in the species list for the project.
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For me the overlap to count as “in” a project area would probably be around 70% or so, but that might have to change depending on if the species is a mobile or sessile one. For mobile species if they’re adjacent to the project area they’re likely found inside it too (you just didn’t catch them there at that particular time). Same holds true for sessile species too, but that’s far more subject to the micro-habitats available and things like that.
The status of the species would not affect the “in/out” of project decision. It’s those very species that fall into high risk categories that we need the information on. Where I work there are a number of terrestrial NT, VU, EN, and at least on CR species (the primary species - the Cat Ba Langur - I work with is CR and at least one other in the area should probably be moved to CR, but not enough work has been done on it yet to properly assess it), plus a number birds (such as the Spoon-billed Sandpiper) that pass through falling in all those categories as well. Given that we are here specifically to protect those threatened species we need the information on them. It does far more good if we have access to them than any potential threat including them serves. Indeed, the people poaching know the species and area well enough that we are constantly playing catch-up as they know far better than us where those species are to be found.