I think that is poor design by the development team. You're not giving the power user any choice in the matter, it's either automated or not at all.
Which brings up my next questions...
Why have you removed the Startup Programs submenu from the System Tools area of jv16 Power Tools X?
And its ability to create backups of changes made within the Startup Programs within this same submenu?
This is one of the main reasons why I use Power Tools in the first place...the ability to pick and choose which programs run at Windows startup.