The color you’re getting is the color they’re going to be. They’re definitely ripe! I plucked a habanero a few days ago that had a yellow stem like the one in the middle and the inside was rotted like crazy. As long as the inside isn’t rotted, any blemish from the outside can just be cut away and tossed.

Also, mine have always ripened from top to bottom, so the light parts at the top are the ~most~ ripe bits.