We normally use 'like a duck to water' only after some form of TAKE + 'to' + noun/pronoun/gerund. Also, there is more to 'taking to something' than just getting used to it.
If you want to paraphrase it you'll have to say something like, "He immediately liked it (and enjoyed/was good at it) just like a duck encountering water for the first time".
Even if the expression did mean just 'get used/accustomed to', you'd need changes in your versions:
1.2. He got used to it like a duck does to water.
1.3. He accustomed to it like a duck does to water.
1.4. He took a liking to it like duck does to water.