Digging up a month-old thread as we have the same issue. Being in California, our client's store is open until 5:00pm however Shopify pushes all orders after 4:00pm to the next day. This makes reconciling deposits a nightmare. After speaking with Shopify Retail Support today, they created a feedback ticket but there's no timetable on when something can be implemented to fix this. I hope they take a hint from almost every other gateway/processor and allow merchants to specify their 'end of day' times as this is a major business hassle.
I do not know which accounting software you use for this but we have the app for syncing Shopify orders to QuickBooks online. It is called QuickBooks Bridge. (https://apps.shopify.com/quickbooks-bridge)
The normal version of the app syncs individual orders to Quickbooks and then when the payout comes, it creates a transfer JV from the holding account to a bank account.
But another modified version of the app, create individual orders only once a payout from Shopify has been received. In that app it considers the Shopify fees in each order and works pretty seamlessly.
Do let me know if you would like to know more about the possibility of automating the data entry for the Shopify orders to QuickBooks.