Yes, you can use LimeLM with your in-app purchases.
If he want he can enable other features after another payment, so each feature has his own price and the app can be modular.
The way to do this is to use custom license fields. For example, let's say you have a separate after-market module call "ModuleX". You can create another custom license field called something like "is_ModuleX_available". By default it will be unset, or "0".
Then, if your customer buys ModuleX from your website, you can just enable the module immediately by changing the "is_ModuleX_available" field to "1". In your app you can detect this change and enable the module.
Does that make sense?