The issue may have nothing to do with the run way space but with launcher and storage capacity. In addition no matter how many vipers the Galactica started with, assuming it had a full complement at the start of Saga of A Star World who knows how many actually have survived the various battles and returned to the Galactica. The same can be said for the Pegasus. Her entire fleet was destroyed at the Battle of Molachy so I highly doubt they have anywhere near a full complement either.
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