I have understand what you were trying to said. This settings are all coming from woocommerce. But I will request you to please contact with this issue with woocommerce team. They will help you with a suggestion or something else.
I do not totally agree, your plugin translates the settings of woocommerce to the front end
So in the form for adding a product in the dashboard when adding a price with teh comma as a seperator for two decimals as set up in Woocommerce is not translated well in the code i guess. It keeps showing price with a dot as decimal seperator. And the price that is not correctly saved at first is an update issue on the dokan end of the plugin i would say.
If you do not agree please tell me what to ask Woocommerce in this case?