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Probably 4 possibilities:
1. Lots of idle time (e.g., from lower demand)
2. Lots of downtime (probably less likely, >90% uptime reported)
3. High dose (100 mJ/cm2 or more), which would require a suitable resist process, but also would have more secondary electron dose (blur) as well
4. @Tanj has brought up an interesting interpretation of multiple layer exposures per wafer. 40 wph could be 120 wph averaged over three layers, for example. Not quite the expected number of layers, for sure. Or even a single layer with multiple (e.g., 3) exposures, still odd.
We also haven't considered R&D wafers, which might also be substantial, e.g., resist characterization.