When multiple mongods on one machine log events with different timestamps, do we really know in what order they executed these logging statements? If not, can we create a logging mode (enabled only in certain test suites) that provides this guarantee?

Besides ensuring that all mongods use the same clock, also consider logging higher-precision timestamps.

Note: there is also the problem of multiple mongods logging events with the same timestamp. We guess that if the timestamp is high-precision and the clock is shared among mongods, that events with the same timestamp can fairly be considered "concurrent". If several events have the same timestamp, then run the trace checker on the execution traces resulting from each possible ordering of the apparently simultaneous events, per Jard & Bochmann 1983 "An approach to testing specifications".