Who is starting xbindkeys?

I have found that xbindkeys is automatically started if you have an .xbindkeysrc in your home folder or in a system folder such as /etc. Hence why it does not usually need to be added as a separate startup item once installed.

This is explained well in the file /etc/X11/Xsession.d/98xbindkeys, which is generated by any normal install from the Ubuntu package. Here is a snippet from the file, generated by running cat /etc/X11/Xsession.d/98xbindkeys:

This file is sourced by Xsession(5), not executed.

PROG="/usr/bin/xbindkeys"
NOAUTO="${HOME}/.xbindkeys.noauto"

This file autostarts xbindkeysrc if the user (or system) has a config
for it AND does NOT Have a .xbindkeys.noauto in his homedir.

[The rest of the file is a script]

So, the simple solution is to take note of the instructions and place a file named .xbindkeys.noauto in your home directory, and then xbindkeys won't start up with your x session, and you can place an alternative startup entry for it with your specific needs.