The PCIe interface is a full duplex communication (like you mentioned bidirectional), however when talking about the standards the specification is measured in a single direction. For example:
So you are correct, the single lane speeds are mentioned as the baseline measurement, then scale to 4, 8, 16 lanes. In teaching this, I give the single lane speeds on a per revision basis, then tell students to multiple by the lanes used for a given revision. I then remind the students that this is a full duplex communication so in theory it would be double the for each lane's base speed.