While I agree that there is a very distinct possibility that Shahs have their origin in local "pahadey" tribes rather than the so called Rajputs and being of Rajput lineage probably could be just a myth propounded to showcase racial superiority, I have to Subodh Kumar Singh's arguments are weak at best.

When Prithvi Narayan Shah said, if he said at all, he is Magar king, he could very well have meant that he is the king of Magars.  Magars, who are the inhabitants of Gorkha and Lamjung, were his subjects and made it possible for him to conquer rest of Nepal.  So, although he was of different stalk, he could very well have identified closely with them, having fought battles together.

This is the first time I am hearing that Magar kings married Tharu princesses.  Be that it as may, PNS marrying a Tharu girl does not prove anything conclusively as most of his matrimonials - I believe he had quite a few - were political alliance driven.