Hello,
You can perform an email override to not send the order creation email when the status is just "created".
Because you have two kind of plugins, the payment can be made when the order is created or later ; that's why you have two different workflow.
It's not related to HikaShop but how the payment gateway are working (like if they need an order id, etc).
Regards,
Jerome - Obsidev.com
HikaMarket & HikaSerial developer / HikaShop core dev team.
Also helping the HikaShop support team when having some time or couldn't sleep.
By the way, do not send me private message, use the "contact us" form instead.