I have come across similar situations before so I can explain how a lender could make this work. The most important item is presumably DTI (debt-to-income ratio) and qualifying income. In theory, DTI may be somewhat tight, but lenders will have ways to make it work.
Using the flex cash towards the $2,500 monthly payment for the ATV is significant because it immediately decreases monthly obligations, thus decreasing DTI. If overtime or bonuses are consistent, lenders also look favorably on the employer verifying overtime or bonuses, thus count towards qualifying income. Roughly increasing the down payment decreases budget for loan, which positively affects monthly payments and DTI.
Other items are builder concessions and closing assistance, and the strong 780 credit score helped provide flexibility when looking at rates. However, all of these adjustments should make it work “on paper” - again, if not tight for DTI.
Once the employment comes back from checking for verification, that is when the lender will recalculate using income, debts and credits will be considered where all of that comes together, and I think you will see that it meets or is with margin. It sounds like when it is submitted your lender understands what they are doing and just were trying appear to out on paper.
