I don't think it would be any different. Whatever you observed when running non-native resolutions will stay true. How much it bothers you only you can know.
With that said - I hardly think 1600x900 can have an advantage over 1366x768 for movies. Typically, either the movie is 1366x768 or less, or it is 1920x1080, in which case 1600x900 is also not enough.
If 1366x768 is truly more comfortable for you in your work, and if you have been unhappy running non-native res in the past, I'd just get a screen with 1366x768...
Current: X220 4291-4BG, T410 2537-R46, T60 1952-F76, T60 2007-QPG, T42 2373-F7G, X61 7673-V2V
Collectibles: X32 w/ IPS Screen, A31p w/ Ultrabay Numpad
Past: Z61t 9440-A23, T60 2623-D3U, X32 2884-M5U