The shutter is always connected to the AF Sensor activation but when set up for BBAF the AF system no longer sends controls to the lens. So yes, the AF detection system is still enabled when you press down on the shutter but if you've disabled focus on your shutter release the lens does not actually refocus. If your lens really is continuing to refocus you should be able to hear it when you depress the shutter or you can test it by prefocusing on something close or very far, recomposing so that everything in your viewfinder is completely out of focus and the depressing the shutter. If the captured image remains out of focus then the camera is not re-acquiring focus when you depress the shutter. If everything snaps back into focus then for some reason the AF has not been disassociated with the shutter release.
Also if there's a sufficiently in-focus image element under the selected focusing spot then the white focus confirmation dot will still appear as the AF sensing system is still enabled but that won't change the actual lens focusing once you've disassociated focusing from the shutter release.
The red focus square on playback simply tells you which focus point was selected in the viewfinder, it does not tell you the image element that you actually focused on before recomposing. IOW, that red square in playback should be the same square you selected when in Single Point or the center of the selected area in one of the Dynamic Area modes, the same as what you viewed through the viewfinder which of course won't be over your subject once you recompose before shooting. IOW, the camera isn't smart enough to know and save the portion of the image you focused on, it just shows which focus point was selected at the time the shutter was released regardless of where that sits in the frame and regardless of what you actually focused on before recomposing.
Does that make sense?
Bottom line, when you do focus and recompose shooting the red focus point square in playback doesn't tell you anything about where you actually focused the image prior to recomposing.