Just made three sloppy clips at:
The cleans has first track with guitar plugged into the line-in of the amp.
If you observe the tone is slightly muddy and lacking in treble.
The second track has guitar plugged into the guitar-in port.
I deliberatly kept the mids high, to get a tone closer to the line-in. However if you notice, the bass and mids are still less than line-in, and treble and presence is more.
Used TRI-AC on Plexi.
First track is sansamp to the guitar-in. The tone has huge high-end. The low end gets removed.
Second track is the same sansamp to the line-in port. Observe how the tone is more bassy and slightly muddy.
Same as above. Used the Boogie setting on the sansamp.
Conclusion: the tone coloring section of guitar amp reduces the bass, removes the muddy mids, boosts the treble and presence.
BTW, I kept the settings on teh sansamp exactly same. So that you can hear the huge difference.