Is there a way to separate multi-select values with a line break?

Use a formula text field with REPLACE()

Do you mean when you retrieve the values into the PDF using freeMarker? I think I did something like that recently, like this: ${record.custbody_my_multiselectfield?replace(" ", "<br />")} Not sure if that will work for you as-is (even if you put your own field ID in) but I think something similar to this approach will work.

Oops I forgot what it's for. Email template

In that case user transaction.custbody_something or entity.custbody_something, etc. instead of record.custbody_something. Also I think the " " in the replace built-in might need to be a different character to avoid breaking on spaces in a single value's name.

I found a NS article that suggests this isn't possible. I had to create a non-stored custom field with value from the multi-select field where I was able to format it the way I want