Why are some chemicals packaged in incompatable containers?
The shrinkage is called panelling and bottles that are otherwise incompatible are made compatible by a process called fluorination. In fluorination the HDPE is exposed to fluoride gas with precise control in time, temperature and pressure. This exposure converts the outer layers of polyethylene to a highly fluorinated polymer similar to teflon.

$$\ce{-(C2H2)_n-~+ 4 F2~~ \longrightarrow ~~-(C2F4)_n-~ + 4HF}$$

This fluoropolymer coating greatly reduces diffusion of the solvent into the plastic and thus the solvent is unable to soften the plastic, preventing paneling.