How to store multi line config in .env?

It doesn't look like it is possible. First off, the .env file is processed on a line-by-line basis and unless the line has an equal sign (=) it isn't considered to hold any information about a variable. Second, .env is not a PHP file and so will not be considered by the PHP parser meaning that the heredoc syntax won't be evaluated to the string you need.

In the case of storing an encryption key, I don't think the line breaks are a MUST, so you could try it out as one long line of text without line breaks. See if that's useable by the encryption functions you're using.