Ardour's playback is aligned to master-out:
"When the playback clock reads 01:00:00:00, the sample corresponding
to 01:00:00:00 is audible at the speaker(s)"
When exporting, and grabbing data from output ports, the signal
is offset by the master-bus physical playback latency. This was
compensated for, but lead to initial silence in the exported file.
New approach is to start capturing export data during pre-roll,
at the time when playback is written to the output buffers.
To also shaves off a common offset to make this work with
realtime export. Effectively this emulates processing with
disconnected master-output port, while still keeping any
latency of effects on the master-bus itself.
Last but not least: jack updates latencies when freewheeling,
(setting HW latency to zero). The callback arrives asynchronously
some time after enabling freewheeling, but after Export
Ports have been configured. Those callbacks are ignored.