*My experience* has been that when replacing the intake seals with the James blue gaskets (with the flange) is that when you replace with those, without rotating the engine, it is very tricky to get them in place. When I did it (without rotating the engine) the fit was very tight and I could not verify the seals were in correctly. So, I went back to the stock seals.
The flanges should not bend unless you over torque them, regardless of seal type/brand, etc. I just did them snug/finger tight with a touch of blue locktite on the threads (probably unnecessary) to prevent the nuts and bolts from backing off due to engine vibration.