I’m still a novice when it comes to JMRI. It is a really powerful bit of software but lacks a bit when it comes to documentation. This is especially so in the area of scripting. Still… more of that later.
A simple way of regarding the inputs and outputs that JMRI uses is to regard all inputs as sensors and all outputs as turnouts (points). It’s a simple terminology but easy to get ones head round.
On Key Hernan most of the inputs are TOTI sensors that report whether a section of track is occupied or not. It does this by sensing traction current is being taken by a section of track. This is usually because a locomotive is in the section. Other sensors could be press buttons or switches on a control panel. The turnouts can be actual turnout mechanisms (servos or solenoids) or signals, level crossing gates etc.; in fact almost anything that needs to be physically moved.