So ssh works fine through console/terminal, but when I am using a MySQL database client (Sequel Pro), it seems to somehow be using a different ssh version, and the include directive therefore doesn't work. It states that it is using the proper SSH version, but does it switch at some point during the protocol?
OpenSSH_7.5p1, OpenSSL 1.0.2l 25 May 2017
debug1: Reading configuration data /Users/me/.ssh/config
debug1: Reading configuration data /Users/me/.ssh/devops
debug1: Reading configuration data /Users/me/.ssh/defaults
debug1: /Users/me/.ssh/defaults line 4: Applying options for *
debug1: /Users/me/.ssh/defaults line 76: Applying options for ch-pre-bastion
debug1: /Users/me/.ssh/defaults line 80: Applying options for ch-pre-*
debug1: Reading configuration data /usr/local/etc/ssh/ssh_config
debug1: Control socket " none" does not exist
debug1: Executing proxy command: exec ssh [email protected] -W 52.33.83.63:22
debug1: permanently_drop_suid: 502
debug1: identity file /Users/me/.ssh/id_rsa type 1
debug1: key_load_public: No such file or directory
debug1: identity file /Users/me/.ssh/id_rsa-cert type -1
debug1: Enabling compatibility mode for protocol 2.0
debug1: Local version string SSH-2.0-OpenSSH_7.5
/Users/me/.ssh/config: line 1: Bad configuration option: include
/Users/me/.ssh/config: line 2: Bad configuration option: include
/Users/me/.ssh/config: terminating, 2 bad configuration options
ssh_exchange_identification: Connection closed by remote host
You have probably more SSH versions installed on your machine and the one from proxy command is probably picking up the old one, without Include support.
debug1: Executing proxy command: exec ssh [email protected] -W 52.33.83.63:22
Try to find a complete path to ssh binary and use it in the ~/.ssh/config of ProxyCommand or just use ProxyJump option, which should choose correct ssh instance`.