Dear Aditya,
thanks for the comments; they are interesting, indeed.
I think you have quite well understood our essay. The issue you point out it is an actual one, namely how to discriminate the philosophical prejudice from the rest of the theory. This is in fact, the diffcult part. However, there a re ways to do it, by means of a clear falsifiable formulation of the "prejudice". If you read the section about quantum physics, you can see what I mean by this. Kochen-Specker and Bell's theorems are two pivotal instances of this process. They found a way to put to the test some ideas which were considered a prioori assumptions in the philosophical background. What I assert, is also that if we assumer a "pre-falsificationist" methodology, namely an empiricist one, it is virtually impossible to achieve this. It it the theory which guides our experiment to test theories.
Your essay surely provide also interesting views (I have very positively commented and rated it!), yet I am concerned with the actual practice of scientists, as also Popper partly was.
Thank you again for your contribution.
Good luck,
Flavio