It is not about foreman_remote_execution itself, but more about smart_proxy_remote_execution_ssh. The version shipped with 2.5 was using an ancient version of net-ssh (pure ruby implementation of ssh), in 3.1 we threw that away and switched to using the ssh binary present on the system instead. I recall there were some issues with the previous implementation and config options like ProxyJump. It is quite possible that the previous implementation just ignored ProxyCommand on its own, while the new one honors it.
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