Steps to reproduce:

1. Download
   https://cdn.zabbix.com/zabbix/binaries/stable/5.2/5.2.5/zabbix_agent-5.2.5-windows-amd64-openssl.msi
2. Set Command Line like this:
   "/i zabbix_agent-5.2.5-windows-amd64-openssl.msi ALLUSERS=1 /qn /norestart /liewa $LogApp HOSTNAME=$hostname SERVER=$zabprox SERVERACTIVE=$zabprox ENABLEREMOTECOMMANDS=1 TIMEOUT=10 LISTENPORT=10050 ENABLEPATH=1"
3. Open zabbix_agentd.conf after the setup

Result:
See part from zabbix_agentd.conf file:
### Option: AllowKey
#   Allow execution of item keys matching pattern.
#   Multiple keys matching rules may be defined in combination with DenyKey.
#   Key pattern is wildcard expression, which support "*" character to match any number of any characters in certain position. It might be used in both key name and key arguments.
#   Parameters are processed one by one according their appearance order.
#   If no AllowKey or DenyKey rules defined, all keys are allowed.
#
# Mandatory: no

### Option: DenyKey
#   Deny execution of items keys matching pattern.
#   Multiple keys matching rules may be defined in combination with AllowKey.
#   Key pattern is wildcard expression, which support "*" character to match any number of any characters in certain position. It might be used in both key name and key arguments.
#   Parameters are processed one by one according their appearance order.
#   If no AllowKey or DenyKey rules defined, all keys are allowed.
#       Unless another system.run[*] rule is specified DenyKey=system.run[*] is added by default.
#
# Mandatory: no
# Default:
# DenyKey=system.run[*]

### Option: EnableRemoteCommands - Deprecated, use AllowKey=system.run[*] or DenyKey=system.run[*] instead
#   Internal alias for AllowKey/DenyKey parameters depending on value:
#   0 - DenyKey=system.run[*]
#   1 - AllowKey=system.run[*]
#
# Mandatory: no

### Option: LogRemoteCommands
#   Enable logging of executed shell commands as warnings.
#   0 - disabled
#   1 - enabled
#
# Mandatory: no
# Default:
# LogRemoteCommands=0
The switch does nothing at all.
Expected:
AllowKey, DenyKey and EnableRemoteCommands are configured according the command line arguments.

If ENABLEREMOTECOMMANDS=1 is still valid, I would expect AllowKey=system.run[*] to be set.

But I think this CLI switch should not be used anymore.

Instead I expect the docs to be updated and to implement AllowKey and DenyKey as command line switches.

As of today, the 5.2 docs still list ENABLEREMOTECOMMANDS=1 

https://www.zabbix.com/documentation/current/manual/installation/install_from_packages/win_msi