Defining the pagination yourself shouldn't change anything.
It might help if you explain why you need to use jQuery to append the pagination component. Normally you just insert your custom component into the appropriate location on the page or inside another component.
I've got three custom components which will be displayed using a tabbing navigation. Each of these components uses a custom pagination.
If I put these three component into my page, the pagination logic of one component will collide with the others, because they using the same "page"-parameter.
My approach was to only load one component, depending on the selected and active tab and to remove the others.
