That's what I'm doing too - time my strokes with the wave's top and stay centered, relaxing my bottom a bit, to absorb any natural tendency of the boat tilt and not letting that get my upper body out of balance. The waves will push you sideways a bit as they pass under, if they are steep, so you should in fact anticipate this to some extent and move with the boat. That part is a bit tricky as each wave is different... I'm still working on it
But time in the seat and taking every opportunity to practice in beam seas appears to be the only remedy... That, and a more stable boat, he-he...
Actually, I have a further question related to paddling in choppy water: do you guys shorten and quicken or lengthen and slow-down your stroke to gain a bit of extra stability? This is different form timing the stroke to the waves as there your timing is related to the waves. Here, the timing can't be adjusted well, because the water is unpredictable and messy, so I am responding with my stroke to chaotic dis balancing forces, so to speak. In this case, if I can't time it, I'll just increase the bracing component in each stroke to have a "crutch" in the water at all times. Yes, wasteful of energy, but better than stopping to paddle in order to brace all out... Both quick and slow seem to work for me and I have not yet figured out which does better... The shorter and quicker strokes give you more opportunities to brace, each responding to a new disbalance. The longer stroke just keeps you stable longer during each stroke... Kind of averages out in terms of paddle time in the water, not clear which one moves me faster and with less extra effort...