By just setting the equation numbering to "(1.1)", Typst cannot infer that you wish to have the current heading number there. You need to specify that separately, via a numbering function:

Doing this will give you the numbers (1.1), (1.2) and (2.3). You see that the equation number also needs to be reset at the start of each section. To achieve that, you can update the heading counter in a show rule for level-1 headings:

#show heading.where(level: 1): it => {
counter(math.equation).update(0)
it
}

These two pieces together will then give your expected numbers. To do the same for figures, just copy the first piece (to set the numbering) for figures, and include the counter updates for the various figure kinds in the show rule:

counter(figure.where(kind: image)).update(0)
counter(figure.where(kind: table)).update(0)
counter(figure.where(kind: raw)).update(0)
// + any custom figure kinds you use in your document

One side effect of this is that if you now reference equations, you no longer get something like “Equation 1”. Instead, the parentheses of the equation numbering is included, resulting in something like “Equation (1.1)”.