Yes, it's safe to do with lithium ion batteries as long as you use the right potting compound (potting compound isn't just one thing). There are compound specifically designed for battery encapsulation that assist with thermal management and preventing ruptures. As the person you're replying to has already stated, using potting compound to fill in cavities and discourage tampering on electronics is a standard practice.

Depending on your design requirements you can also use different battery chemistries or cell constructions to minimize the need for mechanical venting.