Exact same setup here though I realize I didn't quite state it directly, the cottages are owned by individuals but all rented out through the agencies.

We got a much steeper discount, I'm assuming because we were solidly in shoulder season (a couple weeks after kids return to school in North Carolina, and during hurricane season), which the vacation rental company accounts for in their seasonal pricing, but VRBO didn't seem to. At this beach in particular, it is a summer vacation for families and you get a steep drop in prices if you don't have to schedule around school holidays, but VRBO didn't price that in in the same way that the local companies do.