The real problem, at least from the perspective of a contributor, is that the standard isn't really very standard.  Each publication seems to follow their own version or modification of the "standard manuscript formatting".

And what about people who were subbing stuff before the days of e-subs?  I actually sent a handful of mainstream poems and a fantasy story or two out, with no real success, in the early to mid nineties.  They were all sent via "snail mail" back when that was the only real option.  (I didn't even have an up-to-date computer back then.)   They were all formatted in "standard manuscript formatting", at least as it was laid out in the then-current Writer's Market (or guide, or whatever it was called).  Today the desired formatting may be a bit different, especially when it comes to on-line publications or electronic submissions.  I've even noticed some subtle differences between what was in my old Writer's Market book, what was in a much more recent edition, and what I've seen posted on-line as the standard manuscript format.

It's actually taken me a bit to adjust to the formatting found on certain on-line publications, and I still have a tendency to do such things as put two spaces after my periods.  I've seen at least one on-line publication that wants one space after periods.  Underlining instead of italics was indeed the standard for manuscript formatting, but I have seen a change in that.  Some editors still want underlining for italics, while others want italics formatted as italics.

The best you can do is state very clearly what formatting you want, especially if it difers from the established standard, and perhaps even give examples of the things that might not be clear.  Of course, expect there will be at least some material submitted in a different format than you desire. 

And I agree with Mike about guidelines - after you've looked at about a hundred different guidelines, they do all seem to blur together.  It gets difficult to keep straight which publication wants what formatting.  That's why I always double-check the guidelines as I'm sending submissions.  Of course, we're all human, and we all make mistakes.

A final note - keep in mind that much of this standard was developed in a time when most writers typed their manuscripts.  You couldn't do italics as easily fifteen or twenty years ago as you can today.  With most typewriters, it wasn't even an option.  The objective of the standard seems to be to make the manuscript appear typed, and have a fairly consistent look, even with the introduction of efficient word processors and fancy fonts.  Old habits (and preferences) die hard.