The article states they had seat assignments together on the original flight. Of course, when they were put on standby for the next one, they lost their seat assignments and the GA presumably gave them whatever was available when clearing the standby list. Rather than board and attempt to swap seats they seemingly asked to be put on a later flight and AC acquiesced.

With regard to the check-in time issue, the only thing I can think of is they had checked luggage (makes sense, they were moving) and due to the length of line-up it was past T-45 when they made it to the counter. But yes, 90 minus 30 does not equal 45.