ft_min_word is a setting of the MySQL server. In case of hosting server, you cannot therefore change it in the ini_set (which isfor PHP). The server is a seperate thing, and if your host has multiple users using the same server (which is standard on a shared server), they will use the same setting.
The same goes for a .htaccess setting: this can only change how apache will react (if allowed to change), not how the database server is configured.
The variable, described here in the manual is not a dynamic variable that can be set in runtime
So you can try :
Check the length of the search term, then, if it is less than allowed by ft_min_word, use LIKE('%searchterm%')