Following the rule of Formats says you must follow print if there are a variety of paragraph styles within a text.
A friend used to tell me that "a good transcriber's note covers a multitude of sins". If you could come up with a good transcriber's note that explains how you have changed the format, that might be an option. If you can't come up with a good transcriber's note to explain what you want to do...you probably shouldn't change the format. 🙂 I know this text is huge (close to 1000 pages, right?) and adding all those blank lines for blocked paragraphs could add cost to the final document. The requestor can ALWAYS ask for something done as they would like...it's an agency decision. Sometimes we, as transcribers, have to fight back because we know that following the rules is a good idea...and sometimes we don't.
Just a side note: if you are ever taking a formats exam; follow the rules 🙂
Cindi