The package MariaDB-common-10.2.12-1.el7.centos.x86_64 includes the file /etc/my.cnf
This file has the line "!includedir /etc/my.cnf.d"
This package does not create the directory /etc/my.cnf.d
This conflict causes programs such as percona toolkit to fail with an error similar to
"Can't read dir of '/etc/my.cnf.d' (Errcode: 2 "No such file or directory") "

You should either remove this line from the default my.cnf, or include the directory in the package.