Changing an existing API is painful, especially so for cases like this that have existed for a very, very long time.  Such as a change would likely have a detrimental effect on long-standing code relying on the existing behavior.

The module itself is all about "comparing files efficiently" and most of its code is about bypassing direct file reads.  The original purpose of the module seems to be about providing shallow compares, so your suggested change goes directly against the grain of the module and its original intention of being "fast by default".  The docs are very clear about there being trade-offs between correctness and time.

If the module were just being released, you might have a good case (in general, the safest options should be the default); however, the time for this decision was a very long time ago.   This ship has already sailed.