I ran your experiment and here is what happened. I tried the pop up flash first using the 50mm 1.8, in AV mode with 1.8 as the shutter setting. I had ISO at 400 from a previous shot, so just left it there. The final readings were aperture 1.8, ISO 400, speed 1/6. I then switched to manual mode and set those same readings, then fired another shot. Camera info indicates identical readings for both exposures and they both have equal amounts of light when I look at them. I would say they are identical. I tired the entire set up again with the speedlight and the results were the same. However, I did notice that when I was dialing the aperture setting of 1.8, the flash compensation meter indicator was moving by itself as the size got wider and wider. So, am I just noticing some sort of self-correction feature that the camera wants to use because it thinks I'm going to over or under expose a shot? But if that is the case wouldn't it still have to come off -2 if I manually forced it to do so?
Ok sounds like you are misunderstanding how the Canon flash system works. It IS different than with a Nikon camera so, while people are trying to be helpful, it may have confused you further.
When you adjust exposure on a Canon camera it is adjusting the exposure for ambient light. Flash exposure is entirely separate. So in M mode if you adjust the aperture it is telling you how your shot is being exposed compared to what the camera thinks is correct. The needle being in the middle is "correct". Something correct isn't "correct" however, like when shooting a child in the snow(the camera will underexpose) or a graduation where most of the stage is dark(the camera will overexpose). This is probably the needle you saw moving back and forward.
Exposure compensation is only used in Semi-auto modes(Av, Tv, etc). This setting will brighten or darken your exposure relative to ambient light. It does not care about the flash being used(except that it will usually half the exposure to account for the flash on the subject to not overexpose him/her.
To get to flash exposure is different on every camera. However, on the more advanced cameras there is a flash exposure button on the top of the camera near the settings LCD. When this button is pressed you will see the same exposure compensation bar but with a lightning bolt next to it. Adjusting this adjusts how the flash is metered off the subject. When the camera uses the flash it detects the return light off what it determines is the subject(usually either the center of the image or the focus point depending on the camera) and dials in the flash accordingly. If this doesn't brighten the subject enough you can dial in positive correction and if it blinds the subject you can dial in negative correction.
There is a FEL (flash exposure lock) feature on all Canon cameras that can be used to minimize the amount of FEC(flash exposure compensation) you have to use. To use this feature, find the button for it(usually the * button when the flash is up). If you press this button the flash will fire and a * will appear in the viewfinder. This feature meters the flash before you take the shot. You see, if your subject is not in the center of your picture, the flash may not exposure for the subject you want. So you flash the center focus point over the subject and press the FEL button(*). You may have to then hold this button down but sometimes the setting will be held in memory for a specified duration in time(usually the case). You can then reframe the shot and take the image. The picture should be much better exposed.
Flash on a Nikon system interacts with the normal exposure compensation. It's not better/worse, its just different. If you use a Canon its best to think of them as completely separate settings.
For example:
You are taking a picture of a friend in front of a sunset but the friend is too dark - increase flash exposure compensation(or use the FEL feature)
You are taking a picture of a friend in front of a sunset but the sky is too bright and you can't see the sunset but the friend is nicely exposure - dial down the exposure compensation(NOT flash exposure compensation).
I hope this helps. Please let me know if you have any questions or difficulty understanding this post. I realize I covered a lot of topics here and flash is not easy to understand initially.
