I tried to reproduce this on the current build and could not.
On origin/main bfec2754b8, added two cases to apps/server/src/git/GitManager.test.ts (each uses real git): an origin with only main, a local-only branch stack-parent, and a child branch feature/child pushed to origin. Case 1 creates the child the way a new-worktree thread does (GitVcsDriver.createWorktree with baseRefName 'stack-parent'); case 2 sets branch.feature/child.gh-merge-base=stack-parent. Running the create_pr stacked action sends createChangeRequest with baseRefName 'stack-parent' in both cases (vp test run src/git/GitManager.test.ts -t "does not open a PR against a base branch": 2 failed, 'expected [ 'stack-parent' ] to not include 'stack-parent''). Not run in the desktop or web app: the GitHub provider calls GitHub's REST API directly, so a real Create PR needs a scratch GitHub repository and a create-PR request, a forge write this step may not make.
Closing as not planned. If it still happens for you, reply with the exact steps and the version you are on and it will be looked at again.