A couple years later, I have found the answer in documentation for MySQL 5.7:
For MyISAM search indexes, the 50% threshold for natural language searches is determined by the particular weighting scheme chosen. To disable it, look for the following line in storage/myisam/ftdefs.h:
#define GWS_IN_USE GWS_PROB
Change that line to this:
#define GWS_IN_USE GWS_FREQ
Then recompile MySQL. There is no need to rebuild the indexes in this case.