In general, the Bypass mechanism only stops incoming MIDI messages to the MIDI Out block from being sent out. It does not disable controlling the plugin via parameters
Sure – we actually had to think about this one for a bit — wondered for a moment whether Bypass should apply to parameter changes but we decided that Bypass should really only apply to incoming events.
One way around this issue would be to use a script or even a scriptlet (if you have GP4) to control whether events should be sent to the MIDI Out block