I have had a 3.4.10 instance for a while and recently setup a second instance of 3.4.12.
I update various settings in the default.properties file to not be the default on both the server and clients. One example is I generally use:
server.jetty.port = 19880
After running an install.sh --client the port is set correctly for both 3.4.10 and 3.4.12. But after running ctl-setup, the port is back to 8080 in the various configuration files for 3.4.12, but is still the correct 19880 for 3.4.10.
The documentation for ctl-setup says "initial configuration default values are maintained in ctl-defaults.properties" This doesn't seem to be true for either 3.4.10 or 3.4.12 in the instances I've looked at, which always list 8080. I have not yet tried using the --key=value flags as a possible workaround.
This server.jetty.port isn't actually listed in ctl-default.properties (framework.server.port is), but framework.email.mailhost is listed in both default.properties and ctl-defaults.properties and has the same behavior for me.