It seems like the Display Suite module completely ignores
hook_process_node(). Is this the case?
If it is so, what is the way to make minor changes to the final rendering with access to all the node variables?
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Display Suite does indeed hijack the node rendering to a point where the default preprocess functions may not be used.
The module comes with a set of its own preprocess functions that are documented in ds.api.php.
In this case,
hook_ds_pre_render_alter() can be used instead of the
hook_preprocess_node() to modify the output via the complete render array. Also, the
$entity object is available with all values.