Sorry but, began to be dark is different from it was drawing towards evening so it was sunset already.
A look into the Hebrew will help you to understand what is being said. Compare צָּלַל (
tsalal) used in Nehemiah 13:19 with חשֶּׁ ך (
ḥoshek). The latter refers to darkness without light. Consider the following verses.
Genesis 1:2 (ASV) – “And the earth was waste and void; and darkness (
ḥoshek) was upon the face of the deep: and the Spirit of Elohim moved upon the face of the waters.”7
Joshua 2:5 (ASV) – “and it came to pass about the time of the shutting of the gate, when it was dark (
ḥoshek) that the men went out; whither the men went I know not: pursue after them quickly; for ye will overtake them.”
Job 12:25 (ASV) – “They grope in the dark (
ḥoshek) without light; And he maketh them to stagger like a drunken man.”
Job 18:6 (ASV) – “The light shall be dark in his tent, And his lamp above him shall be put out.”
The verses above refer to a different kind of darkness than Nehemiah 13:19. Genesis 1:2 establishes the true meaning in that it was darkness that existed before light was created.
Notice Joshua 2:5 in which the gates were shut when it was dark (without light). This, no doubt, refers to shutting the gates at night whereas Nehemiah 13:19 refers to shutting the gates at sundown when twilight was about to begin. As soon as the shadows were gone, that was Nehemiah’s signal to close the gates. Shadows disappear the moment the sun sets. Nehemiah closed the gates the moment the Sabbath began.
Another use of tsalal is found in Ezekiel 31:3.
Ezekiel 31:3 (ASV) – “Behold, the Assyrian was a cedar in Lebanon with fair branches, and with a forest-like shade (tsalal), and of high stature; and its top was among the thick boughs.”
Here, tsalal refers to shade or shadows accompanied by light rather than total darkness.
Also you misapply inductive reasoning with Passover and Day of Atonement. They are the only two holydays to be observed at sunset: therefore this does not negate when the day starts. And if you look at the context of Genesis 1:1-5 you will see that the first things God made were the heaven and the earth and time. In the beginning signifies that before time was created only eternity existed. So we have time, space (heaven), and matter (earth) as the first three creations. Otherwise if we read vv. 2-3 it will sound like that the earth, the darkness, and the waters were pretty existent with God: which we know is not true as God made all things and nothing existed before He did.
Everything from verses 1-5 was created on day 1. You want to believe light was created first, but Scripture shows the heavens, earth and water were created before light. Therefore, Elohim created those things while it was dark.
I know blasphemy sounds like such an ancient word in our modern times but, you did blaspheme in stating that God worked in the Darkness and not the light after He tells us to not work or walk in the darkness.
YHWH can work whenever He wants. He can work Himself or He can command others to work in darkness. Did not He, Gideon and the Israelites work at night to defeat the Midianites? YHWH delivered them into Gideon's hands that night. Do not the watchmen work at night guarding the walls and city of Jerusalem? Do not confuse working at night with working in spiritual darkness.