Most linear experimental design problems assume homogeneous variance although heteroskedastic noise is present in many realistic settings. Let a learner have access to a finite set of measurement vectors $\mathcal{X}\subset \mathbb{R}^d$ that can be probed to receive noisy linear responses of the form $y=x^{\top}\theta^{\ast}+\eta$. Here $\theta^{\ast}\in \mathbb{R}^d$ is an unknown parameter vector, and $\eta$ is independent mean-zero $\sigma_x^2$-sub-Gaussian noise defined by a flexible heteroskedastic variance model, $\sigma_x^2 = x^{\top}\Sigma^{\ast}x$. Assuming that $\Sigma^{\ast}\in \mathbb{R}^{d\times d}$ is an unknown matrix, we propose, analyze and empirically evaluate a novel design for uniformly bounding estimation error of the variance parameters, $\sigma_x^2$. We demonstrate the benefits of this method with two adaptive experimental design problems under heteroskedastic noise, fixed confidence transductive best-arm identification and level-set identification and prove the first instance-dependent lower bounds in these settings. Lastly, we construct near-optimal algorithms and demonstrate the large improvements in sample complexity gained from accounting for heteroskedastic variance in these designs empirically.