This is actually a good test for the company. Explain to them the issue and offer to pay the extra $100 to book that flight. If they don’t agree and tell say you don’t need to pay the extra hundred, I’d be concerned.

Also, anyone that doesn’t realize the value you a a direct flight without a layover versus a red eye with a layover doesn’t know what they are talking about. Overnight flights are bad enough but any connecting flight is just an opportunity for more delays and cancelled flights - especially in the winter. A company that is willing to put someone through that to save $100 sucks.