You need to charge tax on freight mentioned in invoice whether it is a interstate or intrastate supply.
Tax rate should be tax rate charged on principal item.
It is a composite supply, in fact freight cost is part of value of your outward supply.
You can add to the cost of product itself or show separately in invoice similar to how you show products with tax rate and tax value.
I will have an article with video very soon once get enough time (its audit season) on how to prepared invoice using KYG-INVOICING.