What do you mean by "mixed together"?

PR#2 will show only what changed between dough and toppings.

If you merge it, it will become part of PR#1. You turned the dependency into a single block.

So, if you don't want to mix, you should merge the dependency (dough) first to main (or whatever is your target).

Codeberg probably also supports the same thing, it's a git thing not a GitHub thing. That's why I'm saying it works exactly as expected. Git alone already supports dependencies, and GitHub just follows it.

To block the merge, you can make a workflow that turns PRs with dependencies into drafts. However, as it is a merge from one PR into another, I don't see the reason to. You can easily de-merge them if you need.

From the looks of it, it seems that you are branching at the wrong point, and creating two PRs to main, one of them containing duplicates. That's not what I suggested.