Juan Carlos might have expressed the wish not to be buried in El Escorial, but instead in Seville next to the Catholic Kings.

OTOH, Q.Sofia alledgedely took the decision to be buried far from JC, in Tatoi in Greece, next her own family.

If the emerit king and queen would express such wishes say in their wills, can Felipe VI oppose and decide they should be buried in the Escorial amongst the previous kings ?

AFAIK the Royal Crypt is full (not sure if the Counts of Barcelona will occupy the last places or if there is not even room for them).