No, per instance (or VM if you wanna think it that way) regardless of pipeline workers. If you set it to 100/sec, it will allow 100/sec whether you have 1 worker or 4 workers or whatever.
Now, regarding the automatic adaptation it's not that straightforward. You'd need to adapt your configuration on-the-fly, probably by pushing new config files and using the automatic reload feature.\
So you'd need to calculate
total expected rate / number of instances as a throttle rate for each instance and change the config value each time a new instance is created or killed. Depending on your workflow and provisioning tools, it can range from pretty easy to slightly cumbersome.