Similar for /e/. Strictly 'bed' is /bɛd/ in standard English, but since a true /e/ is not spoken in most Englishes, /e/ is used for /ɛ/.
/r/ and /e/ are used for phonemic transcriptions - again, on the assumption that English is being discussed, and that /ɹ / and /ɛ/ are intended.
I agree that it's done for convenience, and that sometimes the practice could lead to misunderstanding. I also agree that it's annoying for perfectionists, linguistics students, and English speakers who do use these sounds. If one is all three, I imagine it would be hard to live with!