Having two facilities greatly increases the costs to operate the service, too. TTC estimated about 20 years ago that it cost them $3mil per year to "run" a facility, regardless of its size - and no doubt this number is higher today. This was just for heating, lights, etc. - and not the actually provision of service.
In the case of the Skytrain network, because their network is so much larger they came to the realization that the cost of the second facility was outweighed by the additional deadheading of equipment that was required, and so they made the decision to build the second yard.
Dan