Your second lesson has a nastier cousin in TileSets, and it cost us a shipped pack last week.
Our Godot importer declared 492 tiles. Godot built 468. The 24 missing tiles were in the sheet, and a buyer couldn't reach any of them.
The cause was tiles whose declared atlas footprint was larger than the actual art. We already had a validator for exactly that, but it only ever ran on the offender list of a different check, so a one cell tile that declared two by two was never compared to anything.
What found it was making Godot do the counting. We now load the resource headless and assert the built tile count against the manifest. Validating the manifest against the sheet can't catch this, because in that failure both halves agree with each other and only the engine disagrees.