>>Was that normal or a suggestion that the ship was too low in its waterline?<<
Define what was meant by a "few feet above the water." I've seen photos of the ship and there's nothing about any of the porthole arrangements which were inappropriate, ill advised, unusual, or of such poor design that they didn't meet the requirements and safety standards of the day.
What was brain-dead was running the ship in the fog...with none of the watertight doors closed as required by Canadian Pacific's regulations...and which Captain Kendell inadvertantly admitted to during the inquiry which followed. Had they been closed properly to begin with, the ship still would have been severely damaged, but in all likelihood, she would have remained afloat.