magic number of 5000 is default number of open files that mysql configure as one of the limit
/* Try to allocate no less than 5000 by default. */
limit_3= open_files_limit ? open_files_limit : 5000;
you can read more about the logic in this function. adjust_open_files_limit() of MySQL.
Why XB ignored setting in [xtrabackup] section ? I will let XB team answer it but I can tell you how you can get your limit set.
xtrabackup: open files limit requested 100000, set to 200000
[mysqld]
open_files_limit=200000
[xtrabackup]
open_files_limit=100000
So eventually [mysqld] limit is honored though that will also alter limit for normal running server.