When we use the word transparent we usually intend that something is passed on from one place to another without being looked at, or that it can remain unchanged. Sometimes also transparent is intended.
In other words, when we move data around, we are being transparent by not looking at it while the data itself can be opaque in a computing sense, as it can contain anything and we don't need to know about it.
One good reason to be transparent is to be capable to carry binary data without encoding overhead.
We sometimes use the word transparent where we mean opaque and vice versa. That's because the two semantically opposite words are being used in the same context and frequently intend the same feature.