The exterior of my mod required me to alter the navmesh for the exterior cell its connected to (generally a no no I know, but I don't plan on making it an esm, and Beth has fixed many issues so I don't care). What are the standard, safest procedures for finalizing, generating cover, etc. for exterior cells connected in Skyrim?

My mod works fine at the moment without finalizing (I believe I did once before but have had to change it again since), so should I even bother? I'm just wondering cause the CK is telling me to.

Make sure all the vertexes line up between the cells. Overlap them. Check the Navmesh using the Find Triangle button. When there are no errors, check cover (Find Cover Edges button). And then Finalize.
If all the edges are bright green and your door links are light green, you did it correctly.

Don't forget some errors don't show up until you leave the cell and return. It seems like some others also don't show up until you save. Do those things before you finalize if you make extensive edits.