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There are two kinds of export in Qtractor:

a) Track/Export Tracks - this works as a mix-down (for audio) or merge (for MIDI) of your complete session arrangement; track solo (S) and mute (M) takes effect on which tracks are mix-down/merged into the export audio/MIDI file; current clip selection doesn't apply here; any inserted audio fx plugins are processed so take track export here as a faster-than-real-time bounce recording.

b) Edit/Clip/Export... - this applies to one clip at a time and thus takes current clip selection into account; only clip properties (gain, pitch-shifting, time-stretching) take effect here; track plugins are not; it's kind of a file copy process only.

the kind that you should be interested in, to emulate clip merge, is the first kind, MIDI track export.

Seeya