It makes sense, but in the end, Isabel became the mother of a king.
With other kings (and NOT kings) being taken into El Escorial, it seems odd that the founder of the dynasty would not have a proeminent place at the spanish royal pantheon.
I seem to recall once reading somewhere that Felipe V disliked the Escorial and much preferred his palace at La Granja which he rebuilt in the style of Versailles, his childhood home. Maybe the fact that he would have been separated from his wife if he had followed custom and been buried at El Escorial was also a factor. At La Granja he and Isabel Farnese could be buried together in the same tomb.
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