I use the hub[0] cli tool to manually specify the branch when I create a PR.
https://marketplace.visualstudio.com/items?itemName=GitHub.v...
pr !open "$(git remote -v | grep origin | grep push | cut -f 2 | cut -d " " -f 1 | sed -e "s|git@\(.*\):\(.*\).git|https://\1/\2|")/pull/new/$(git rev-parse --abbrev-ref HEAD)"