Zabbix shipped conf files have the include statement in the middle of the file, and this creates inconsistent behavior.
For example, this is the order of parameters in zabbix_server.conf:

LogFile=/var/log/zabbix/zabbix_server.log
.......
.........
Timeout=4
LogSlowQueries=3000
...
Include=/etc/zabbix/zabbix_server.d/*.conf
...
StatsAllowedIP=127.0.0.1
EnableGlobalScripts=0

If I then create zabbix_server.d/my_zabbix.conf with contents:

Timeout=10
EnableGlobalScripts=1

Only Timeout=10 parameter will be overriding the default configuration.