Yes, I taught about defects, or binning, as this usually is the case with other devices line multi-core CPU, where they disable some defective cores. The thing is that it's logical with CPU, which have very clear cut boundaries between the core (use the whole core, or disable it if there's a defect in it). But in FPGA there's no such boundaries. The compiler will spread the design across the whole FPGA. If a gate is not functional, then they can nos simply bin it as a lower gate count part, as any design is free to use any of the gates. So, I don't think this is because of yield problem.
You are right, looking at other parts, there are a few others that are similar, like EP2C15/EP2C20, EP3C5/EP3C10, etc!
If you look at Cyclone V E, the A2 and A4 also has the same size, but they differ in IDCODE. Same goes for Cyclone V E A5 and Cyclone V GX C4/C5 (the latter having transceiver, although here, it could be discarded as A5 due to defective transceiver).
Interesting!
Thanks.