Ladder to DNA using Transformation Matrix
You can't perform this transformation by applying constant transformation matrix to the ladder model since it's not linear transformation like joojaa said in the comments. What you would have to do instead is to define the transformation as a function of height as you have done in both of your proposals.

So both of your proposals are kind of correct, except for the typo in second one where you should use $R$ instead of $T$ that you raise to power of y. However, you might have difficulties raising a matrix to non-integer power (requires expansion of Taylor series, AFAIK), so your first proposal is much more practical.