rosdep not limiting dependencies correctly on ros2 src install

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I am trying to build ROS2 foxy from source on Alpine linux. I have added a lot of rosdep keys into the rosdep distribution files and changed rosdep to use my repository (I am testing it before I make a PR). I am following the Linux install from source instructions except I only want to install ros_base dependencies. The source instructions try to install deps and compile every package. I checked out the ros2/variants package that defines what ros_base actually is and am trying to use that as the 'package'/'stack' to calculate recursively the dependencies. However it keeps suggesting installing irrelevant packages, and gives me errors about packages I don't care about (desktop).

bash-5.0# export
declare -x HOME="/root"
declare -x HOSTNAME="cfdae4a75db0"
declare -x LANG="C.UTF-8"
declare -x LC_ALL="C.UTF-8"
declare -x OLDPWD
declare -x PATH="/usr/local/sbin:/usr/local/bin:/usr/sbin:/usr/bin:/sbin:/bin"
declare -x PWD="/ros2_ws"
declare -x ROS_DISTRO="foxy"
declare -x ROS_PACKAGE_PATH="/opt/ros/foxy/share"
declare -x ROS_VARIANT="ros_base"
declare -x SHLVL="1"
declare -x SKIP_KEYS="console_bridge fastcdr fastrtps rti-connext-dds-5.3.1 urdfdom_headers"
declare -x TERM="xterm"
declare -x http_proxy="http://172.17.0.2:3142"
bash-5.0# pipenv run rosdep install --from-paths src --ignore-src --rosdistro ${ROS_DISTRO} --skip-keys "${SKIP_KEYS} desktop" src/ros2/variants/${ROS_VARIANT}
ERROR: the following packages/stacks could not have their rosdep keys resolved
to system dependencies:
desktop: No definition of [rqt_common_plugins] for OS [alpine]
ros2doctor: No definition of [python3-rosdistro-modules] for OS [alpine]

To reiterate, the 'src' directory is the all the repos for the foxy distribution.

bash-5.0# pipenv run rosdep check --from-paths src --ignore-src --rosdistro ${ROS_DISTRO} --skip-keys "${SKIP_KEYS} desktop" src/ros2/variants/${ROS_VARIANT}
System dependencies have not been satisfied:
apk spdlog-dev
apk py3-catkin-pkg
apk eigen-dev
apk py3-pytest
apk py3-babeltrace
apk py3-numpy
apk console_bridge-dev
apk tinyxml-dev
apk cmake
apk curl-dev
apk py3-empy
apk qt5-qtbase-dev
apk pkgconf
apk py3-pytest-cov
apk clang
apk py3-lttng
apk py3-lark-parser
apk freetype-dev
apk libx11-dev
apk libxaw-dev
apk libxrandr-dev
apk mesa-dev
apk freetype
apk qt5-qtbase
apk opencv-dev
apk tinyxml2-dev
apk py3-mock
apk uncrustify
apk assimp
apk py3-matplotlib
apk yaml-dev
apk py3-netifaces
apk clang-extra-tools
apk py3-lxml
apk py3-cryptography
apk py3-psutil
apk py3-pydocstyle
apk py3-qt5
apk py3-pycodestyle
apk sqlite-dev
apk openssl
apk cunit-dev
apk py3-mypy
apk py3-pytest-mock
apk py3-flake8
apk tango-icon-theme
apk py3-pydot
apk py3-graphviz
apk py3-pyflakes
apk bullet-dev
apk cppcheck
apk zstd-dev
apk cppunit
apk libxml2-utils
apk log4cxx-dev
ERROR[desktop]: No definition of [rqt_common_plugins] for OS [alpine]
    rosdep key : rqt_common_plugins
    OS name    : alpine
    OS version : 3.12_alpha20200428
    Data:
_is_ros: true
        osx:
         homebrew:
           packages:
           - ros/foxy/rqt_common_plugins
        ubuntu:
         focal:
           apt:
             packages:
             - ros-foxy-rqt-common-plugins

ERROR[ros2doctor]: No definition of [python3-rosdistro-modules] for OS [alpine]
    rosdep key : python3-rosdistro-modules
    OS name    : alpine
    OS version : 3.12_alpha20200428
    Data:
debian:
        - python3-rosdistro-modules
        fedora:
        - python3-rosdistro
        gentoo:
        - dev-python/rosdistro
        openembedded:
        - python3-rosdistro@meta-ros
        rhel:
        - python%{python3_pkgversion}-rosdistro
        ubuntu:
        - python3-rosdistro-modules

What am I doing wrong that it wont correctly filter down the system dependencies to a recursive search on ros_base?