This is one of the busiest railways in the world. Highest possible utilization of tracks. The dynamic Cab Signalling system makes sure you're not running into another train.
It's a very good idea on the NEC to learn the signals! Cab signalling only changes aspect when you pass the signal, and in many cases you should be reacting when it first comes into view.
It's not uncommon, although you typically see it more around choke points such as the North River Tubes and the Portal Bridge. The ability to "stack" multiple trains in a block allows more trains per hour on a section of line, and also lets multiple trains occupy single station platforms. Here's a couple photos from the New York area showing stacking in action on both Metro-North and in Penn Station. Somewhere online is a photo of four or five trains stacked within a block awaiting to enter the North River Tubes from New Jersey, but I couldn't find it.
Slight off topic, but this image shows how cool Harlem Line could be in TSW if we had the missing rolling stock. It feels so empty with just the M3A and the M7As.