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Thank you for responding to my questions. So, who was supposed to be stopped on a siding, and who was going straight through? Did one of the trains actually ever go onto the siding? (since they both appear to have been on the main track and had a head on)
Could the engineer have left the siding, and gotten back onto the main track without noticing a whole sequence of lights, and wouldn’t crossing the ‘switch’ have at least have generated something similar to going over a speed bump?

Are ‘lights’ the only thing the engineer depends on before leaving a siding?

1.The UP train was to enter the siding with the commuter continuing on the main track.

2. No, the UP didn't make it to the siding before getting hit.

3.As the UP train hadn't entered the siding he didn't have a chance to exit and enter the main track.

4 It looks like the signal the commuter would have seen is somewhere beyond the station, this is very common signal displaced as the signals are usually located to protect a switch telling the engineer that he is either going straight on the main, leaving the mainline or in some cases holding the main while another train enters the siding. No, no speed bumps but I understand that some railroads are trying new technology that will stop a train if it passes a signal.

Now that I have bored you to death, one minor point about sidings. It isn't unusual for a siding to have a "derail" device protecting the main in case a engineer forgets and tries to re-enter the main without the proper signal.