tl;dr
If the package you try to configure has the ability to do configuration via a JavaScript file, you can add the renaming at the beginning of it:
process.env.PERCY_TOKEN = process.env.CYPRESS_PERCY_SALESFORCE_TOKEN;Explanation
While this isn't the solution I was looking for, it is a workaround for this specific use case. Percy supports JavaScript config files so I migrated my YAML config file, then I logged process.env and the .env file's variables were there, so I just need to copy the correct one. This might work for other packages that support JavaScript config files (or some alternative kind of hook/preloader where custom code can be placed), but if they don't, then the question is still unanswered.