Even if it has been around ever since, the scriptmodule opens a separate config path outside the config ini and it is not transparent to the user that some flags are hardwired in the scriptmodule.
I understand that this may cause some confusion, but as I said, I'm not aware of any reported issues related to this.
I ditched the initial idea to have exactly one config source thus, to have any config switch set in/get from the scriptmodule as it would be a royal annoyance to rewrite the evaluation/precedence logic of the config ini in bash.
I don't see why would be necessary. Ultimately the dialog based UI maintained in RetroPie is just a wrapper over the CLI options, meant to be used by users who don't need many options besides maybe turning on 'video' downloads. Avanced/experienced users are using the CLI to scrape and can (and do) ignore the UI. For the former users, the current .cfg is (ubenknownst to them) the config.ini, since they just use a couple of options to scrape and don't seek or need other parameters.
As a compromise I would see that the all applied switches from the scriptmodule are prompted to the user before he/she starts the scraping and/or have the skipped flag also configurable.
Yes, I can see this working - start anew without any .cfg so the user would always need to set the parameters and those parameters (including the skipped flag if we don't want to default to a safe value) are not persisted to any configuration. We can make also make it more clear that options set in the UI override the config.ini options.