Can it be used to covertly run computations invisible to the OS or CPU?

Only to the same extent that any other co-processor add-in card can do stuff that's not observable by the CPU. Your CPU's RAM is managed by the CPU's memory controller hardware, and that memory controller does not give software the ability to issue individual DRAM commands like precharge. This research uses a memory controller implemented on a FPGA, talking to its own pool of RAM.

This research requires a custom memory controller that's doing "weird" things, the CPU isn't really getting involved here. It's very different compared to row hammer in my opinion. If you have a custom memory controller then I think all bets are off.