The state of the "Enable MIDI Output" would only be saved for the plug-in instances saved in the template, not for new instances of the plug-ins. This is why I would use track templates to add the synths rather than load them up in a project template.
The "Enable MIDI Output" setting is based on the value of generateEvents in the VST Inventory entry for each plug-in. With X3 the value defaults on if generateEvents is 1, prior versions would only enable the check box. The generateEvents value is set during the plug-in scanning process. Other than editing the registry and changing the generateEvents values to 0 for the plug-ins that have the value set to 1, I know of no way to alter the default "Enable MIDI Output" behavior when adding new instances of plug-ins. Of course, anytime the VST Inventory is reset&rescanned or a plug-in is updated triggering rescanning for the plug-in, the generateEvents would need to be edited again.