Of the multiple cnf files in /etc/mysql/conf.d/ dir, which would be the last one to be read (and will eventually take precedence)?
If I understand it correctly, there can be only one config file. But mine ends with

#
# * IMPORTANT: Additional settings that can override those from this file!
#   The files must end with '.cnf', otherwise they'll be ignored.
#
!includedir /etc/mysql/conf.d/


and so it is directly responsible for "merging" those additional ones into itself.

The !includedir directive is covered in the manual https://dev.mysql.com/doc/refman/5.5/en/option-files.html which states:


  There is no guarantee about the order in which the option files in the directory will be read.


So it probably depends on the OS and filesystem but you should not depend on it anyway, even when it seems "stable" for now.

I sugget using the !include directive instead and maybe a different folder for those config files where the order matters.