When you're creating InDesign articles that target phones, it doesn't really matter whether you use 640x1136 or 750x1334.The content will be scaled to fit on any phone. On iPhones, there will be minimal letterboxing, such as 1 pixel. There might be a little more letterboxing on Android phones if you create an Android app. Feel free to create different layouts and check the article size and appearance. I think you're find that there's very little difference between 640x1136 and 750x1334 articles.
As a general rule when creating fixed-layout (InDesign-based) articles, create 768x1024 articles for tablets and 640x1136 articles for phones. You then need to create a different structure (two top-level collections) with different articles for phones and tablets in your app.
Another option is to create responsive HTML articles that work well on all devices, both phones and tablets. Then you only need one structure for your app.
Would it be a good idea to make the resolution for each device the largest that there is then?
For example make the phone 1080x1920px, the iPhone 6+ resolution. And make the tablet 1536x2048px, the iPad Air and Retina iPad resolution? We are not making one for the iPad Pro because it is a different screen size ratio.