Based on some conversations internally, a call that transfers out of the In-queue Call Flow should not be tracked as an abandon, but a disconnect would be.
If you want to know for sure, though, you would need to open a case with Support and supply Conversation IDs for calls that show as Abandons (might get tricky trying to track down an abandon to a specific call).
Something you can try, though, is modifying the In-queue Call Flow so that instead of a Disconnect to end the flow, you use a "Transfer to Flow" action, and transfer it to an Inbound Call Flow that just disconnects the call. That way, the call should end with a flow-out rather than an abandon (presuming that Transfer to Flow succeeds...which it should.)