Clean user profile, every log in?
The dock is being populated with default items by way of /System/Library/CoreServices/Dock.app/Contents/Resources/en.lproj/default.plist.  This is protected via SIP though.  So you can try the obvious (and non recommended) method of disabling SIP to mess with the plist.  There are other options.


Use dockutil in a login script to add/remove/etc. whatever icons you desire.
Customize the dock as you want it to be, and copy ~/Library/Preferences/com.apple.dock.plist. Have a login script replace the default
dock plist with the backup, then kill the dock and maybe cfprefsd.
Management suites, such as Casper, can manage the dock
remotely.  


See https://www.jamf.com/jamf-nation/discussions/18357/el-capitan-user-template-dock-customisation-issue