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Qtractor computes the latency based on the jack settings, and offsets the audio tracks accordingly ?
almost. it's not quite correct it is based on jack settings but on state information jack gathers from chained/connected ports.

depending on the jack version and flavor, this latency information might not be dynamically available, so that a minimum of one period of latency is always applied.

and yes, the audio recording latency compensation work in qtractor is just about offseting recorded audio clips accordingly. you can always tweak by hand the clip's offset if it doesn't get it perfect ootb ;)

cheers