I’d like to gently point out that — just like there is no monolithic “publishing industry” — there is no “standard manuscript format.”
He goes on to provide specific examples of formats from other sectors of publishing, and specific elements that vary between genres or publishing sectors. So, yes, a disclaimer I failed to make in my original post was that I was talking about the genres of science fiction and fantasy in specific, and somewhat more generally and with less authority, about fiction submissions.
Actually, in the case of electronic submissions, I don’t think there’s a “standard manuscript format” yet. I’ve seen submission guidelines that want manuscripts in specific fonts, specific font sizes, specific file types, etc. And they can vary widely from market to market.
This is also true. Many electronic markets have specific submission requirements, and there is not a great deal of standardization between them. I strongly prefer to attach a .rtf or .doc/.docx file to a submission, because that preserves my print-oriented standard manuscript formatting, and is also the least amount of work for me. But not everyone’s online content management system supports file attachments. And many people are rightly wary of accepting executable files (ie, Word macros) from random persons on the Internet. Hence the varying requirements of online submissions.
Which are, frankly, fairly irksome to me. Going through and replacing all my underlined (for italics, obviously) text with _these characters_ is annoying and easy to make mistakes on. Then the next market wants *asterisks* or something. For me personally, this tends to simply discourage me from submitting to those markets at all. The extra effort is a barrier to entry, and it doesn’t feel to me like a shibboleth of professionalism, as the basic print-oriented standard manuscript format does.
As always, your mileage may vary.