I love the saying "I know I'm paranoid, but am I paranoid ENOUGH?"
When I think about drainage, I look for solutions that will manage non-stop monsoons for months at a time.
But a solution that's good enough IS good enough!
And the "best" engineering is what gets the done with minimum cost and resources. Now instead of expending huge amounts of labor and effort to solve a bugger problem than it was, you can spend all that on MORE features and plants!
Congratulations! Especially for keeping a sense of proportion and seeking the most practical solution.
It sounds like your review for that contractor could be a good one after all! Along the lines of "when problems were discovered later, he DID make it right."
If you happen to recall, a few months from now ... might you post an "after" picture of how great it looks?
(I'm relishing my mental image of the REST of your yard under 2-3 feet of water, with waves and seagulls and a fishing trawler cruising by, but THAT BED is high and dry!)