Guidelines are just that: guidelines. They guide the development of your application, they do not make all of the decisions about your application. They document the best thinking about design at the time that the guidelines were written. They help you make a better application by focusing your time and attention on the decisions that matter to your specific application instead of wasting time arguing about toggles versus checkboxes.
There are great reasons to follow guidelines. Consistency across applications makes it easier for users to use your application because they can anticipate how it will look and feel, and they can build upon the expectations for behavior that they learned in using other applications. Likewise, guidelines can help your application feel like it fits into your mobile environment, thus making users more comfortable with it.
There are great reasons to not follow guidelines. Guidelines are written for application development in general, and they do not always work for a specific workflow. Guidelines can get outdated if they are not updated in a timely fashion, and thus can lag behind current best practices.
If you choose not to follow guidelines, you should be able to clearly articulate why you are not following the guideline. Most of the questions that you have asked can be addressed through user research. A/B testing will answer your question about checkboxes versus toggles. (In this case, since toggles are significantly easier to manipulate on a touchscreen, your A/B testing is virtually guaranteed to come out in favor of toggles.) A simple usability test can answer your questions about accordions and whether you need to show less content to make it clear to your user that they can scroll. If your research indicates that your users are able to complete their task, and are satisfied in doing so, you are probably safe in not following guidelines.
Users don't care whether you follow guidelines. They care that they can do their thing. If they can seamlessly and successfully do their thing with your application, they're not likely to notice or complain about not following the guidelines. If they can't seamlessly and successfully do their thing with your application, they're more likely to notice that you are not following the guidelines. Optimize for the success of your users.