I will answer the questions posted though I'm not sure how much that will help since I do not think you really understand what the camera and flash are doing based on the descriptions given above.
1 & 2. It is not a % difference. The closest approximation for what it is doing is that it is setting the flash exposure compensation to an additional -1 EV. In other words, TTL set to -1 EV flash compensation will be approximately the same as TTL BL set to 0 EV flash compensation.
3. You are using the term flash sync speed incorrectly. Flash sync speed does not vary. It is the fastest shutter speed that can be used that will allow a full powered flash to record on 100% of the sensor/film. (The shutter is fully open when the flash goes off hence lighting the entire area.) I believe the term you are looking for is the shutter speed for the camera's ambient light exposure. TTL BL doesn't impact the camera ambient exposure. However, since it is trying to be 1 stop below the camera's ambient exposure, it does reduce the amount of light coming from the flash based on the camera settings.
4. All modes in the flash except manual exposure produce pre-flashes.
So I will take this description...
Shooting in RAW, I also underexpose by 2-3 stops in-camera and turn the flash system itself down by a further stop.
As you can imagine this results in some pretty dark images, but Nikon NEF's are amazingly tolerant and shadow areas don't seem to suffer greatly when I adjust the exposure back up to where it should be in ACR later.
... and try to describe what is actually happening.
You are setting the camera's ambient exposure to underexpose 2 stops. You don't say if you are doing this with one of the automatic modes or whether you are setting the exposure manually. Assuming you are doing it with one of the automatic settings, that means the camera exposure compensation is set to -2. You are using TTL BL on the flash and using an additional flash compensation of -1.
For the settings above, the camera will set the shutter speed, aperture and ISO as best as it can, within the limitation you've preprogrammed through the various custom settings, to give you an exposure for the ambient light that is 2 stops too dark for the conditions. The flash honors the -2 for the camera, the BL gives the flash an additional -1 compensation and your setting of the flash compensation to an additional -1 means that the flash will light to give the total exposure of -4 stops based on the same metering it used to set the camera. Or the camera is 2 stops too dark and the flash is 4 stops too dark. Of course, the difference between the camera's exposure and the flash's exposure is 2 stops.
So assuming I didn't run into a limitation (shutter speed that can only go so low or so high, ISO that can only go so low or so high, the aperture limitation which can only open so far and the flash which can only go so dim or so bright), the expectation from your settings is that the flash is firing to light 2 stops darker than the ambient light. Of course, that assumes you are using an automatic mode to get your camera's exposure to -2 using in camera compensation. Since the flash uses the camera's compensation setting as well as the flash's compensation setting, there could be a significant difference in how the flash reacts if you are setting the camera's exposure manually and the compensation of the camera is not set to -2.
As a side note... Canon cameras and flashes do NOT react the same way to changes in the setting as Nikon cameras do. And there are also some slight differences in how various Nikon camera/flash combinations will react to the same settings. That is why you don't see much written on the topic.