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In the meantime we have switched from using ament_tools for ROS 2 to use colcon (see design article). For the upcoming ROS 2 release Bouncy we recommend using the new tool - even though ament_tools will still be available in that release.
Unfortunately that mean that we will not spend any effort on fixing issues in the deprecated tool. If you want to look into the problem and try to fix it we would certainly be happy to review / merge fixes. I think the problem is very similar to what was fixed in catkin_pkg recently. Maybe this diff helps.
Using the new build tool you can get a list of all build, run, and test dependencies: colcon info <pkgname>
The result will consider group dependencies.
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