Paginate options in checkbox of a form field
Might be no one will land up here,still adding the answer and foolish doubts I had

The pagination done for query to get options works! .

The reason I was in doubt before was because of using the query results as option of checkbox field, the time I added themed the pager while rendering the form, I got the pager which worked out of the box!

How I figured out if pagination working with the query was by adding ?page=1 in the url manually which changed the checkboxes , it ensured me I just have to theme the global pager :) .