[red-knot] Fix possible TOCTOU mistake in mdtest runner (#15673)
## Summary
Somehow, I managed to crash the `mdtest` runner today. I struggled to
reproduce this again to see if it's actually fixed (even with an
artificial `sleep` between the two `cargo test` invocations), but the
original backtrace clearly showed that this is where the problem
originated from. And it seems like a clear TOCTOU problem.
