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After a bit more digging, I think the issues we have been experiencing are due to the publisher "Throttler" checking the realTime clock instead of the simTime clock

void GazeboRosInitPrivate::PublishSimTime(const gazebo::common::UpdateInfo & _info)
{
  if (!throttler_.IsReady(_info.realTime)) {  // <-- HERE
    return;
  }

  rosgraph_msgs::msg::Clock clock;
  clock.clock = gazebo_ros::Convert<builtin_interfaces::msg::Time>(_info.simTime);
  clock_pub_->publish(clock);

For whatever reason, the realTime is not updated when stepping the simulation. As a result, the gazebo_ros interface never publishes clock updates when the simulation is paused and is being stepped. All other nodes relying on the /clock topic unsurprisingly stop working as expected.

In gazebo_ros_pkgs#1325, I suggest a simple 'fix' of simply changing:

if (!throttler_.IsReady(_info.realTime)) {

to:

if (!throttler_.IsReady(_info.simTime)) {

This does the trick for our purposes. However, it looks like it causes a few build tests to fail. I will try to investigate these to see if they are a concern, and will update this answer if anything comes up.