Sometimes you might work with models whose iLogic Rules have not been prepared for Design Automation. As a result they may throw exceptions when run automatically and would just cause issues.
If your app bundle already has all the info to drive the parameters of the model correctly, without the help of the iLogic Rules in the model, then you can simply prevent them from running automatically. The IiLogicAutomation interface of the iLogic add-in (also used in this blog post) has a property called RulesEnabled that you can set to false before opening the Inventor document or changing properties that could trigger them.