It's possible to combine the linear workflow, i.e. working with regions on the timeline, and the non-linear workflow, i.e. launching clips from trigger slots.
The general steps to do so are:
In the example below, cue A starts at bar 3, followed by cue B at bar 7, then all cues are stopped at bar 11. After that, cue C is triggered on bar 15, then cue D on bar 19, then all cues are stopped at bar 23.
Just like any other markers, cue markers can be repositioned. Moreover, right-clicking on an existing marker allows changing the cue that should be triggered.
The rest of the composition would be written the usual way, by adding consecutive audio and/or MIDI regions to the canvas.
A session that is set up in such a way can be exported just like any other, into a single audio file or through stem exporting.