Sales Invoice - product bundle & tax template inconsistancy over API


We use our custom designed system to send data to create sales invoice via API.
Whenever any item that has a linked product bundle is invoiced, if the sale invoice is set to submit, the Packing List & Tax values from selected Tax Template are not updated and posted without stock ledger entry (stock change) and same with the tax table.

But when the sales invoice is set to save (as draft) the packing list updates the stock item (as per product bundle but tax tables are not affected even when a tax template are selected.

So our current flow is long = custom system > creating draft Sales Invoice > logging in ERPNext > saving Sales Invoice Drafts
We want to reduce the flow to custom system > create Sales Invoice (submitted, with stock update from product bundle, as well as auto set taxes as per assigned/selected tax template)

Do let me know if there is a solution available to this