The histogram and preview image are processed in the camera with all the settings you have enabled in the camera, including ALO, HTP, NR, picture styles, white balance, colour space etc. etc.. Therefore, as far as your raw capture is concerned, you can't believe anything you see when you have ALO and some of these other features enabled.
If you want to get closer to the truth then it is best to shoot with neutral picture style, contrast at minimum, and all gimmicky picture enhancements turned off. I have read that you should also shoot in the Adobe RGB colour space to improve histogram accuracy. If you want to go the whole hog you could even set a custom white balance, often known as "Uni white balance", which will disable the red and blue channel multipliers, so that your histogram is not skewed by white balance adjustments.
Personally I am happy to shoot with neutral picture style and with the gimmicks disabled. That gives me an in camera histogram I can interpret well enough. I look for, and am happy to see, small areas of blinkies, just to show me that I am on the edge of clipping, but not too far into clipping for recovery to get my details back if I need them. If I don't see a hint of clipping then I know I haven't really pushed my exposure terribly hard towards the right. I tried using Uni WB but did not bother with it for long.