I think it might be to just differ between words, but why isn't 殺す こらす, 下ろす 下らす, etc. Is it phonetic change? Is that the reason why 足りる isn't 足るる。For passives, 戻る isn't もだる.
Looks like you've mixed transitive/intransitive pairs, plain/causative pairs and even old/modern pairs.
- Causative forms follow certain grammar rules. It always ends with either -(さ)せる or -す. It can be used with almost any verb, including transitive verbs. Just as the past form of a verb is not listed in dictionaries, causative forms are not listed in dictionaries.
- Transitive verbs are words on their own, and have their own entries in dictionaries. You basically cannot predict a transitive verb from an intransitive verb, although there are some useful patterns. Many transitive verbs (食べる, 殺す) do not have an intransitive counterpart in the first place. While some transitive verbs, such as 動かす and 乗せる, might originate etymologically from causative expressions, this does not mean people today consider them to be causative forms.
- Pairs like 足る/足りる, 流る/流れる, 燃ゆ/燃える are old/modern pairs. They are of course etymologically related, but have nothing to do with transitivity or causative rules.
In summary, your question is essentially about the etymology of transitive verbs. However, like the etymology of many other words, it is fundamentally unpredictable. You need to memorize each transitive verb. This is a different issue from the grammatical rules of causative forms.