It's rather pointless to benchmark Optane SSDs against DRAM. Later this year we'll have Optane DIMMs that aren't constrained by the PCIe bus and will actually be able to demonstrate the latency capabilities of the underlying 3D XPoint media without all the overhead of NVMe and PCIe.

3D Xpoint latency is still several times slower than DRAM. 3D Xpoint also still suffers from limited endurance. 3D Xpoint NVDIMMs will be used as pmem block devices, not as primary RAM.

For DRAM-equivalent latency and endurance you need STT-MRAM, which has already been available in DDR3-compatible DIMMs. Both STT-MRAM and 3D Xpoint will be available in DDR4-compatible DIMMS too but only STT-MRAM will run fast enough and long enough to replace DRAM.

Is PCIe latency that much worse than main memory? I honestly don’t know; I was under the impression that both had latency in the 10s of nanoseconds.

NVMe devices using battery-backed DRAM or MRAM offer about 5µs access time, and current Optane SSDs are under 10µs. (NAND flash based SSDs with RAM-based write caches also have write latency below 10µs.)

So is the bottleneck really NVMe? Could there be a different protocol over PCIe that had lower latency?

NVMe was more or less designed to offer the lowest possible latency for a block storage protocol. You could beat it with direct memory mapping, but then you're limiting compatibility to systems with working 64-bit I/O addressing and storage media that doesn't require complicated management like NAND flash does.

You maybe consider about NVDIMM and persistent memory. But isn't available with consumer client products.