Dear Oddly Obsessed…
There are plenty of industry standards for manuscript formatting. Deviations can distract agents and editors from your brilliant content, so it’s best to format as expected. This item, however, doesn’t require toeing any lines. Even among published books you’ll see both alternatives. So choose the style that feels and looks best for your story. For example, starting new scenes flush left might inject a subtle dramatic oomph that works for the story. Or, maybe you’ve got many different elements peppered within your narrative text, such as emails or handwritten letters, and the visual signal of a flush left first paragraph would help the manuscript’s readers better identify new scenes. Some writers simply like the consistency of indented paragraphs throughout a document. You have personal wiggle room with this item, so wiggle your person at will.