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Is there a special way to use these of which I'm unaware

The way to use those is to tell rosdep that your OS is "*_python3" e.g.

root@cdf6f1d3bd1c:/# rosdep resolve python-serial
#apt
python-serial
root@cdf6f1d3bd1c:/# rosdep resolve python-serial --os ubuntu:bionic_python3
#apt
python3-serial

should we be rewriting such rules to be python3-* top-level rules alongside the python-* ones, as is the now-established practice for new rules?

I believe yes, you would need to use a conditional dependency similarly to https://github.com/ros/ros/blob/ee5469facade6ff917d56ea9340b7c5a90f8f574/core/roslib/package.xml#L31-L32

Note that you will also need to add a python3-serial key to the rosdep database as it doesn't currently exist