The money can't just float. Whatever the seller has agreed to pay toward buyer-side compensation gets directed somewhere on the settlement statement, and your representation agreement is what caps your agent's share of it.
Three things can happen to the difference. It can stay with the seller, which is common if the seller's willingness to pay was negotiated deal by deal rather than published as a flat offer. It can be applied as a seller credit toward your closing costs, which needs your lender's sign-off because loan programs limit how much an interested party may contribute, and those limits are tighter on investment property than on a primary residence. Or, in some states, your agent can rebate part of their fee to you, and a handful of states restrict or ban commission rebates, so that option genuinely depends on where you're buying. Ask the agent directly and get the answer in the agreement.
What you can't do is have the extra handed to you as cash outside closing. Everything moves through settlement.
One practical note on flat fees. If your agreement says $5,000 and the seller side is only willing to fund $3,000, you owe the difference in cash at close unless you negotiate it into the offer. That's the trade for a fixed number. It also means the flat fee only saves you real money on expensive houses, which is exactly your case at 700k, so it's worth asking two or three agents what they'd charge on that price point and what they'd stop doing at that price.
