scripts: pytest: log msec with leading zeros

Milliseconds are logged as is, without leading zeros. This means that
following log content is produced, which is not aligned by columns:

  12:54:27.972:INFO:root: Test message
  12:54:27.992:INFO:root: Test message
  12:54:28.12:INFO:root: Test message
  12:54:28.32:INFO:root: Test message
  12:54:28.52:INFO:root: Test message
  12:54:28.73:INFO:root: Test message
  12:54:28.93:INFO:root: Test message
  12:54:28.113:INFO:root: Test message
  12:54:28.133:INFO:root: Test message

Change milliseconds logging to include leading zeroes. This allows to print
nicely aligned log messages:

  12:54:27.972:INFO:root: Test message
  12:54:27.992:INFO:root: Test message
  12:54:28.012:INFO:root: Test message
  12:54:28.032:INFO:root: Test message
  12:54:28.052:INFO:root: Test message
  12:54:28.073:INFO:root: Test message
  12:54:28.093:INFO:root: Test message
  12:54:28.113:INFO:root: Test message
  12:54:28.133:INFO:root: Test message

Additionally it is much easier to configure programs simplifying
timestamped log browsing (like in logview-mode for Emacs), as it is more
standard and does not require custom regex matching.

Signed-off-by: Marcin Niestroj <m.niestroj@emb.dev>