For those who might understand this stuff a bit more deeply, here is the log output from the Little Snitch installation:
Oct 8 15:24:56 Pegasus Little Snitch Installer[3273]: INFO: Installation mode: Fresh Install
Oct 8 15:25:10 Pegasus Little Snitch Installer[3273]: INFO: *** Stopping Services
Oct 8 15:25:10 Pegasus Little Snitch Installer[3273]: INFO: *** Removing Components
Oct 8 15:25:10 Pegasus Little Snitch Installer[3273]: INFO: *** Stopping Services
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: *** Removing Components
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: *** Copying Components
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Library/LaunchDaemons
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Fixing permissions for directory /Library/LaunchDaemons
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Applications
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Directory has SF_NOUNLINK flag set, leaving alone: /Applications
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Library/LaunchAgents
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Fixing permissions for directory /Library/LaunchAgents
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Library/Application Support
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Directory has SF_NOUNLINK flag set, leaving alone: /Library/Application Support
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Library/Little Snitch
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Creating directory /Library/Little Snitch
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Library/Application Support/Objective Development
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Creating directory /Library/Application Support/Objective Development
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Checking directory exists: /Library/Application Support/Objective Development/Little Snitch
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Creating directory /Library/Application Support/Objective Development/Little Snitch
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Installing LittleSnitch.kext (4718) in /Library/Extensions/
Oct 8 15:25:11 Pegasus Little Snitch Installer[3273]: INFO: Installing Little Snitch Daemon.bundle (4718) in /Library/Little Snitch/
Oct 8 15:25:12 Pegasus Little Snitch Installer[3273]: INFO: Installing Little Snitch Uninstaller.app (4718) in /Library/Little Snitch/
Oct 8 15:25:12 Pegasus Little Snitch Installer[3273]: INFO: Installing Little Snitch Network Monitor.app (4718) in /Library/Little Snitch/
Oct 8 15:25:12 Pegasus Little Snitch Installer[3273]: INFO: Installing Little Snitch Software Update.app (4718) in /Library/Little Snitch/
Oct 8 15:25:12 Pegasus Little Snitch Installer[3273]: INFO: Installing Little Snitch Agent.app (4718) in /Library/Little Snitch/
Oct 8 15:25:12 Pegasus Little Snitch Installer[3273]: INFO: Installing launchd configuration /Library/LaunchDaemons/at.obdev.littlesnitchd.plist
Oct 8 15:25:12 Pegasus com.apple.xpc.launchd[1] (at.obdev.littlesnitchd): This service is defined to be constantly running and is inherently inefficient.
Oct 8 15:25:12 Pegasus com.apple.xpc.launchd[1] (at.obdev.littlesnitchd[3377]): Service exited due to signal: Terminated: 15 sent by launchd[1]
Oct 8 15:25:12 Pegasus Little Snitch Installer[3273]: INFO: Installing launchd configuration /Library/LaunchAgents/at.obdev.LittleSnitchUIAgent.plist
Oct 8 15:25:13 Pegasus com.apple.xpc.launchd[1] (at.obdev.LittleSnitchUIAgent): This service is defined to be constantly running and is inherently inefficient.
Oct 8 15:25:13 Pegasus com.apple.xpc.launchd[1] (at.obdev.LittleSnitchUIAgent[3387]): Trampoline was terminated before jumping to service: signal: Terminated: 15 sent by launchd[1]
Oct 8 15:25:13 Pegasus Little Snitch Installer[3273]: INFO: Installing Little Snitch Configuration.app (4718) in /Applications/
Oct 8 15:25:13 Pegasus Little Snitch Installer[3273]: INFO: *** Starting Services
Oct 8 15:25:13 Pegasus Little Snitch Installer[3273]: INFO: This is a major new install. Configuring appropriately.
Oct 8 15:25:13 Pegasus Little Snitch Installer[3273]: INFO: Updating boot caches...
Oct 8 15:25:24 Pegasus ReportCrash[3379]: Saved crash report for Little Snitch Daemon[3377] version ??? to /Library/Logs/DiagnosticReports/Little Snitch Daemon_2016-10-08-152524_Pegasus.crash
Oct 8 15:25:45 Pegasus Little Snitch Installer[3273]: INFO: done.
Oct 8 15:26:25 Pegasus Little Snitch Daemon[85]: 3.7 (4718): Permissive Mode ON
Oct 8 15:26:44 Pegasus com.apple.xpc.launchd[1] (at.obdev.LittleSnitchUIAgent): This service is defined to be constantly running and is inherently inefficient.
Oct 8 15:26:48 Pegasus Little Snitch Agent[356]: Little Snitch Agent version 4718 started.
Oct 8 15:26:49 Pegasus Little Snitch Daemon[85]: 3.7 (4718): Permissive Mode OFF
Oct 8 15:26:50 Pegasus Little Snitch Network Monitor[510]: Little Snitch Network Monitor version 4718 started.
Oct 8 15:42:11 Pegasus Little Snitch Network Monitor[510]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked
Oct 8 15:45:58 Pegasus Little Snitch Configuration[689]: BUG in libdispatch client: kevent[EVFILT_MACHPORT] monitored resource vanished before the source cancel handler was invoked
I also noticed that some permissions were repaired during the installation, or at least this was reported. That function appears to not be present in macOS Sierra, so perhaps there was something there.