There are various reasons you might pause the build briefly. A short pause lets the previous layer cool slightly... someone (I'm assuming nophead) made a martini-glass type model without inter-layer pausing, and it got sufficiently hot that it sagged, ruining the print.
There's also the possibility of a nozzle cleaning step, whereby the nozzle is driven over a cleaning brush or blade to remove accumulated plastic.
I don't know if manual pausing was done, but it is possible, maybe to feed in new filament for all I know.