You seem to miss the difference between the Swedish and Dutch cases where an heir(less) looses their right to succession upon marrying someone without the needed consent and a morganatic marriage where the heir(ess) remains in the line of succession and as head of the dynasty/monarch has the opportunity to alter things.

When prince Xavier de Bourbon de Parme married Madeleine de Bourbon-Busset his half brother decided she was not equal and the marriage was deemed morganatic. However once Xavier's nephew was head of the dynasty he decided otherwise making the children of that marriage legitimate heirs and Hugo number two in the line of succession.

In Russia we see a similar situation. HIH Grand Duchess Maria Vladimirovna has not deemed the marriage of her son and heir Grand Duke George Michaelovich equal so his wife and children do have the Grand Ducal titles or Imperial styles. Yet she knows perfectly well that once Georgy succeeds he is going to alter the rules around marriages from a certain date (read his own marriage date), making his wife HIH Grand Duchess Victoria Romanovna and their children Imperial heirs.

The same could have happened if Franz Ferdinand had succeeded. Technically his children were already the heirs in Hungary because that kingdom did not have a history of morganatic marriages. So only the Imperial Austrian crown was something that needed to be altered as that part of the double monarchy did know morganatic marriages. By changing the rules (as Archduke Otto did later in his life) Sophie and their children could have become legitimate.