Except when you press the 'External Diff' button in the internal diff tool (in the bottom right pane of the UI).
I have tried multiple external diff tool configurations, even a custom one and none of them respond to Command + D or Action > External Diff. Clicking the 'External Diff' button in the internal diff view does work.
I've only found this to be the case when comparing a remote against a local (the 'Diff against current' option in the tree UI).
Sorry for the previous answer, I realised I stupidly missed the 'except' part about the diff pane button working. This looks like a bug where the higher-level menu function isn't hooked in but the embedded diff button is, I'll fix that. Logged as a bug: https://jira.atlassian.com/browse/SRCTREE-1003
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