Following command is used with timeout specified of 9 seconds:

./bin/zabbix_sender -c etc/zabbix_agentd.conf -s badger_100 -k  🌭 -o   "🌭🌭🌭" --timeout=9 

etc/zabbix_agentd.conf
defines timeout as 2 seconds:

Timeout=2

Question:
What will be timeout used for making a connection ?

Answer:
3 seconds

zabbix@zabbix:~/zabbix$ ./bin/zabbix_sender -c etc/zabbix_agentd.conf -s badger_100 -k  🌭 -o   "🌭🌭🌭" --timeout=9 -vv
zabbix_sender [216639]: DEBUG: In zbx_connect_to_server() [127.0.0.1]:10051 [timeout:9, connection timeout:3]

2 seconds timeout specified in the configuration file was ignored.

Documentation is not helpful:
One sender documentation page mentions that timeout argument exists, but what is it used for is not mentioned.

Another sender link does not mention timeout at all.

So, there are several issues.
1) Sender probably should read timeout file from the config file, if this was specified.
2) It is hard to understand for user which timeout is used for what. The fact there are multiple timeouts and which is defined where and for what purpose. Documentation updates are required.