I did not check what you modified, but the original Plugin Persist 2.0 Scriptlet can already automatically bypass a plugin after an adjustable delay when no MIDI activity is detected. Or did I miss something? 
That’s right, but there is nothing I can do to change this. I can only find workarounds. In fact something happen when the plugin is first initialized, which doesn’t happen when the plugin is “started” bypassed. It seems that this initialization takes a little bit of time which makes the plugin unavailable during a very very very short time, such that the first note played cannot be played. The solution would be to initialize the plugin at loading time whatever if it is bypassed or not. I had a talk with our friend Nebojsa about this, but at this time he didn’t want to change the current plugin initialization because of my Scriptlet, what I can understand.