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I agree with the developer when they say that it’s much better to integrate WP-Affiliate Plugin using Option 2. This is the easiest way.
However, there are times that we need to use OPTION 1 to have more control of the affiliate plugin. You yourselves said that OPTION 2 has drawbacks. Speaking of drawback, I have one. My theme is not that well coded and your SHORTCODE inherited the theme styling. I am at the mercy of the theme developer to integrate the changes to get rid of my problem. Option 2 assumes that your theme is well coded.
I would like to implement OPTION 1. However, for non-coders like me its very hard to modify the header to mimick my main website. There should have been feature or ways for non-coders to implement smoothly OPTION 1. Like there is a menu builder, place to upload logo. Things like these are basic features which developers should include in the plugin feature. Given the fact that these is a plugin and this will be used mostly as 2nd site.
Just my 2 cents.
I have the same issue with integrating option 1. I think making the HOME link in the affiliate plugin as link to my main site is not a good idea. If i do this then, where is my affiliate HOME page then then?
Is there a way to build a 2nd menu to mimic our main website menu so?