No, the buildings were not specifically designed to survive an impact by a large jet plane.
It was after their design was completed that the question was raised whether the buildings would survive an impact (I believe, in part, because of their height) and it was estimated that they would survive the basic impact. To arrive at that, the engineers had to determine what kind of impact (what the plane was doing and what its circumstances were) was expected and then their calculations would flow from that.
If someone proposed, "I have a block of metal (or a metal tank containing the maximum amount of fuel a 707 could carry) weighing what a 707 would weigh and fired it at the maximum speed a 707 could attain into or at a given location where it would do the most damage to the building structure, would the building survive?" is a different proposition from "a 707 trying to locate the airfield in fog, flying relatively slowly, and low on fuel".
Another thing would be, for instance, if one assumes that the contents would be relatively unflammable or very limited amounts or that the fire suppresion system would handle that (a simplifying assumption) so that the jet fuel load would burn out in a matter of minutes but that the contents would not catch fire and be a continuing heat source, one could make a judgement that the effects of the jet fuel would be minimal threat to the survival of the building since the heat source would be gone and, even if the fire protection was compromised, the structure could take that amount of heat. Probably Robertson made that kind of assumption, given his tools available and the kind of impact expected, when he did his calculations and made his conclusions. In light of what happened, it wouldn't be the first time that assumptions, especially about the fire, proved to be incorrect.
In the end the buildings survived the impacts but did not survive the continuing degradation of their structure caused by the widespread and uncontrolled fires.
