Delivery charges appearing on invoice

Yes. It can be recorded in purchases and frieght inward a\c. 

I forgot configuration in tally. Freight inwards has a hsn code this means gst is applicable on the recipient.  So they need an account for that to calculate and offset input and output taxes. Technically, invoice act must be adhered to. If delivery charges are not mentioned get it amended. But it doesnt make any difference if your working on a software because configurations must have been set. 

Ive gone through the tha tax invoice and it doesnt mention any freight at all! These tax people create problems to everyone. But HSN must be mentioned and tax must be mentioned. I think the shop owners will get tired to calculate 2 gst rates. So its all consolidated and your good to go when there is no descripttion needed.

Audit needs evidence. Its the chance an auditor can take. Audit thresholf suggests 3% errors permissable but im not sure about indian threshold. This is not an error but still you need an evidence. But if it is a practice that no need to include freight charges as the performance obligation covers it, then yes its good for auditing. 

I think it comes under composite supply. So, no separate invoice is needed and tax rate can be rate charged for principal supply.

Just for clarification, You cannot conclude that this is not composite supply. When supplier is providing transportation also, it will be a composite supply and tax rate will be the rate of principal supply.