A set of stacked PRs is exactly the same as a line of commits. The only difference is the UI, but the UI is the important bit here because lack of UI is what's stopping folk from doing that today.
Even when I've developed my changes as a stack of commits, I'll feed them to my team one commit (and one PR) at a time so they're easier to review — and I discovered that GitHub had turned on stacked commits UI because for one particular project I'd manually created a set of PRs in advance (with the right bases) and GitHub offered to create a stack out of them.
So instead of solving that problem, GitHub developed tooling around a workaround for that problem (targeting a PR at another branch that also has a PR).
Expanding reviews to allow per-commit reviews avoids the need for managing additional branches and all the headache that comes with it.
The commits in a PR are already a stack of patches, and so PRs are already "stacked" as they are.
If feature X depends on the refactoring (cannot be rebased on the un-refactored upstream), it's part of the change; you can't just merge the feature and not the refactoring.
If the two are separable that way then, sure, it makes sense to ask for them to be separate PRs.
and the changes depend on each other so I can't open multiple independent PRs
Why? Is it a technical restriction? Tightly coupled architecture is not the best solution anyway.