I recently participated in the Ironman Bahrain 70.3 Middle East Champs. The swim was a sea swim which was really quite choppy with strong winds. There were also some noticeable currents as water flowed in and out the bay which had to be taken into consideration.
I have been swimming mostly the TI way (although not exclusively) for a couple of years. My local swimming pool is a leisure pool which during weekends and school holidays has a wave machine which is switched on every 30 mins. This has been helpful in training for me to try different things.
What I have learned from being thrashed around in a wave machine and I felt was proven in a real race is that you cannot fight rough(er) waters, you have to work with it. If you approach swimming the Total Immersion way with an emphasis on good balance and being relaxed you can ride out pretty tough conditions without much additional exertion. You may find you need to rotate a bit more to get a clear breath or modify your recovery over the water slightly but otherwise it should still be a pretty patient stroke. I personally find a high stroke rate (like you may see some elite triathletes doing) doesn't work for me as 1) I get tired quicker and 2) it doesn't seem to match the natural rhythm of the swell/waves. I tend to breathe only to the left when racing and even with the wind blowing into my face on the way back I only had a couple of occasions on the where I missed a breath although I did rotate a little further than normal.
I was using a DeSoto 2 piece sleeveless wetsuit (I find it interferes less with my stroke, particularly around the shoulders) so of course it was even easier to relax and have good body position than swimming in just jammers but I still think balance, relaxation and rhythm are your key focuses for true open water swimming.
Oh and I wouldn't worry too much about the lifting of your head in open water. You need to sight to see where you are going. I sight every 4 strokes (or 2 stroke cycles) unless I am on the toes or under the arm of someone who I am confident is swimming in the right direction. I guess it's a problem if it's causing your hips and legs to drop but if it's not don't worry about it.