> more substantial changes still to come for anyone not grandfathered into a Pro plan

The change applies to existing subscriptions, some paid a year in advance.

You can get a refund, from the article:

> If you hit unexpected limits or these changes just don’t work for you, you can cancel your Pro or Pro+ subscription and you will not be charged for April usage. Please reach out to GitHub support between April 20 and May 20 for a refund.