I'd say it's the opposite. Dynamic languages largely use boxing as the indirection mechanism for their highly dynamic type systems, since it works well there. But boxing isnt synonymous with type flexibility, and Java uses it for other reasons (mostly).
I think that's exhaustive. You can pretty much grep through and remove them from 90 % of coffee with a little refactoring and replacing HashMaps with specialized ones. Only if there's null returns or ConcurrentHashMaps involved does it get tricky.
An array of primitives like byte[] or long[] isn't Byte[] or Long[]. The former don't cause boxing. Maybe you're thinking of ArrayList<Byte>?
That probably occurring hides a lot of complexity. That’s my original point. Optimisations are happening especially when Integer and Long are involved. There are sometimes actually less boxing than you would expect reading the code.