Early thoughts about Holmstedt's article.
The opening word choice "ordered" rather than created, is quite consistent with the chaos leitmotif the author is clearly utilizing.
In response to the odd flow of the narrative, Midrash B’reishit Rabbah 3:8 postulated the cyclical past of numerous creative events followed by destruction. In such a setting "in a beginning" becomes plausible but feels like reverse engineering a solution. Scribal error, combined with reinterpretation seems more likely if the 'beginning' is to be read indefinite.
I favor the second possible translation offered by Holmstedt "In the beginning 'in which' God ordered the heavens and the earth. Therefore, though vs 1 as stand-alone introduction, makes a great deal of intuitive sense in light of modern cosmology, I suspect the author wasn't using the terms 'earth' as a planet but in anthropic focus of usable, productive land, heavens representing the region above as a part of the whole, again with an anthropic focus. If so, vs 1-3 flow just fine. If the process of 'ordering ' the earth and heavens is the intent, this removes the awkwardness of God 'creating" then subsequently creating again.
I know in vs 7 etc. the 'firmament', "of the shamayim" was formed to divide the tehom (primeval chaotic waters) is named shamayim, (which has inspired more questions) but I imagine the author as embracing a looser definition than we impose. Heavens probably meant anything 'above' but from the anthropic standpoint the firmament was the defining boundary whereon the lights of the sky are made to appear. (The term is used variously throughout the OT.) If so, then vs 1-3 read continuously.