zabbix_agentd.conf says "Include=/etc/zabbix/zabbix_agentd.conf.d". AFAICS the subconfig files are read in an unpredictable sequence. If you add or edit a config file, then the sequence of untouched files might change by chance, depending upon the underlying file system.
This makes it very difficult to override a subconfig file (e.g. the company-wide default for all clients) by a local config file. You cannot be sure which config file is read last. To get reproducible results I would suggest to include the subconfig files in an alphabetical sequence, as usual.
Of course it would be possible to add another Include line to the company-wide config file and to introduce another config directory, but sorting the files would be smarter (IMHO).
Probably proxy and server have the same problem.