Vary content based on code

I need to modify woocommerce emails based on coding variables. For example Im using WooMemberships and I want to alter the content between the different memberships.
I was looking todo this directly in the woocommerce email template files, however if I do this will it stop me being ablke to use your plugins with them from an aesthetic point of view?
Are there any options to alter the content by code in your plugin?

Thanks