There is no conflict. It's a settled principle of law that a specific provision over-rules a general provison.
The general provisions are permitted Capital Account Transactions and LRS while specific provision is
"remittance from India for margins or margin calls to overseas exchanges / overseas counterparty " (Margin Trading).
Hence, in a nut-shell, investment in shares,etc. is allowed but trading of assets where entire sum of payment is not instantly due (Futures Trading, Forex Trading,etc.) is not permitted. That will mean that one can buy IBM shares but can not go long on IBM futures.