Creative Speculation

""We looked at every possible thing we could think of that could happen to the buildings, even to the extent of an airplane hitting the side," said John Skilling, head structural engineer. "However, back in those days people didn't think about terrorists very much.""

From your link to the 1993 article in the Times. He's speaking in present tense.
Skilling is being interviewed in that 1993 article, in the times. He is speaking in present tense. He is talking about what was done back during the run-up to constructing the buildings. In that 1993 interview, he is talking about various threats to the building, INCLUDING the study of the 707 scenario, in response to the '93 bombing.

I did make one mistake, I thought the second paragraph from the '93 article was cribbed from a much earlier interview, but it was not.
Still doesn't change the fact that this statement is flat out wrong:

"Mr. Skilling did not reference the 707 study in 1993"

He does, in the italicized excerpt above.