Agent, Kevan Lyon of the Dijkstra Agency uses the word count in Microsoft Word. She has not had editors express an opinion one way or another. So that's she scoop right from the . . . well, that's one agent's opinion--grin.
This is a really tough business to break into, but I suspect that sometimes we make it harder on ourselves than it needs to be. Sure there needs to be guidelines, but there seem to be a lot of people who are NOT agents or editors--swearing that the powers that be will throw out your work if you fail to use the exact 2 acceptable fonts or if you fail to calculate your word count correctly. I try not to feed into that "rule mongering" and just write the best damn book possible.
I'll bet you it's the VERY rare agent that would turn away a stellar story because the author use arial font and underestimated the word count by 2,000 words. Is my impatience and rebel nature showing? Gulp. Have you had an actual experience to the contray?