But that time adds up eventually - and that's before you take into account the need for more specific routings, with some platforms not able to take longer trains - then you may need SDO, the list goes on and on.
The point the quote you were quoting was making was that if you had (say) 8 coaches which could be run as two 4 coach services or one 8 coach service that the 8 coach service would take up less pathing time.
Yes there would be other complications, however with the ability to walk through the whole train and SDO or better still ASDO (both of which are used a lot on the South Western Railway network with little/no impact on reliability) there's not really much of an issue. Yes there would be some costs, but probably not as many as having to cancel services as soon as the timetable falls apart because of a few trains being late. There would also be staff cost savings in that at 6tph they each need a driver and guard, reduce that to 4tph and they still each need a driver and guard but only about 2/3rds the number.
You also have the option to increase frequenties during the peaks to 5tph or even 6tph so that the majority of people would still have a fairly similar service, but with the advantage that it would only be for a short time and possibly only in the direction of peak flow. This would mean that after the peak there were more spare paths to allow you to fix any delays.