It's the other way round. If a root can take both -eru and -aru to derive verbs, the former derivative is a transitive, and the latter an intransitive, verb. Compare B-1-1 and C-1-1 in this list how -eru, taken out of morphological pairs, can be both transitive and intransitive markers.
Also, are all eru verbs that are ending changing ichidan verbs?
The list is very clear that -eru suffix always derives an ichidan verb. The problem, however, is to accurately recognise the boundary between the root and the suffix. For example, kaeru (to return; intransitive) looks like a perfect ichidan verb being derived from the root ka plus the suffix -eru. No, it's a godan verb consisting of kae + ru (the conjugation stem, to complicate the matter further, is, therefore, kaer-).