1. Byte sequence should not matter since you are saving to a TIF, which is a standard format.
2. If the ICC profile isn’t integrated, it means that the data is in the scanner’s native colour space and you can make a custom profile of the scanner. (It is possible that the scanner firmware or app converts the colour space internally but then why would we have the option of not including the ICC profile?)
One thing I would add to the dpi vs bit depth business is that I would rather scan at lower dpi with the native (max) bit depth since colour integrity and gradients are more important to you. Ideally, you would scan at 1200 dpi and 48 bits, then down sample the resolution using a batch script.