You can get around that, but it takes a decent infusion of money... For our intimate, our EM's kept telling us, "You'll have to have a custom if you want that..." and it wasn't true at all! We were able to work around every single problem.
We wanted a private room for dinner, so we booked V&A's private room. Other options that we considered were booking the empty GF Cafe (it was closed for dinners then - not sure if it still is), the empty tea lounge (after the tea service is over, they close that down, too), or a suite like the Cape Coral at the GF. Back in 2002, when we had our wedding, the minimum for a dinner at the tea room was $600, which is really not bad, considering we spent more than twice that at V&A's. I think it was a $1200 minimum for the GF Cafe, and for the suite, it would obviously be the cost of the suite! If you booked one of those 3 options, your event would be catered by GF Private Dining. We bypassed our EM and went directly to private dining, who showed us around the GF, showed us our different options, quoted price minimums for each, and gave us copies of the menu options. The Private Dining department really is the intimate bride's best friend, if you want to do something unique.
As I said, we ended up having dinner at V&A's, and after dinner, we took our guests for an hour long fireworks cruise on the Grand One. That was the perfect way to finish the evening - the weather was beautiful, and the yacht is definitely big enough for a party of 10 or 12. We served bottled waters and chocolate covered strawberries (again, courtesy of Private Dining) while we were on the yacht.
Definitely don't let your EM discourage you into having a wedding-in-a-box. Our 3rd & final EM was Lynn McKitrick, and she was so helpful to us, with all of the extras that we added to our wedding.
Good luck, and let me know if you have any questions for me.
Cheers!
Heather W