When people say Read Option and "Base Offense" or "Base", every body knows its a play and not a formation. So you and others, don't have to keep repeating that. What they're really addressing/saying, is 'when you use or run it too much'. Even players have used the word "base" or "base offense" when addressing it.
Yes, the Pistol offense (which RG3 and Kaep run) is a better formation to use the read option out of, cause the Panthers with the Shotgun (with the back next to Cam), kinda gave it away that is was a running play in several ways. However, if you notice, Russell Wilson and the Seahawks, ran it out of the Shot gun as well. And I think the reason is simple: It's because both Cam and Wilson are more drop back/pocket passers at this stage than Kaep and especially RG3, so there more comfortable and successful operating out of more conventional sets.
And that's how I would like it. I want Cam to develop his drop back/pocket QB skills first and foremost. That other stuff can always be added in or used occasionally (depending on the defense). Cam's going to get enough yards, just on scrambling plays when there's nothing there down field.
I actually don't like the pistol formation for running the read option. The reason the pistol is good for NFL teams is that you can take your NFL offense, put the QB 3 yards behind the center, line up the RB behind the QB.... and then you just run your NFL offense.
The pistol is an easier transition from NFL formations to pistol formations because they are actually virtually the same. So Harbaugh can still run his entire playbook, but add some read option elements to it.
But with a pistol formation you can only really run a dive read option whereas with the shotgun formation with the RB next to the QB you shouldn't tip if it is a dive option or sweep option.
The shotgun formation actually makes it more deceptive, not less.