Hi Nick,
Glad to hear that you like JA Atoms 🙂
Option 1: You're right that JA Atoms supports custom style for Virtuemart only, it doesn't offer custom style for J2Store by default. However, it will still work well with J2Store but it will use default style comes with J2Store. If you wan to have the same look & feel like VM in this template, you will have to customize style for it.
Option2: JA Mixstore is built with T3 framework so it will not work with T4 unfortunately.
Let me know if you have any further question.