The behaviour blocker did actually notice the encryption taking place, however: It decided to let the encryption continue since GPG is a legit tool.
It's more an issue with the way EAM trusts processes. Currently, trust is given on a per-process basis. So GPG for example is either trusted or not, no matter the circumstances. We are currently reworking the way trust works in EAM, so it assigns trust based on a trust-chain. That means, GPG may be trusted when it is started by a trusted process, but not if it is started by an unknown or untrusted process.
So you running GPG in your command line window will be okay, as your command line window was started by Explorer, which was started by UserInit, which was started by WinLogon, which was started by the OS during initialisation, all of which are considered trustworthy. However, a batch script running GPG, would result in GPG not being trusted, as the batch script isn't trusted.
There is no ETA yet for when this change will roll out, but it won't be this year