2D engine design/architecture: model transformations

Hello! I'm working on this hobby little 2D engine in JavaScript because I want to learn how all this things are implemented and architectured in general. Internet is full of resources but most things are mathematical or theoretical stuff, there is very little about implementation or architecture for small 2D engines like the one I'm working in. So, this is my context and at the end are some questions I hope you can help me with:

I have a Body object that has different properties like (pseudo-code):

Body {
    angle: float
    scale: float
    acceleration: 2d vector
    velocity: 2d vector …