Does Prince Manuel of Bavaria have succession rights to the defunct Bavarian throne? He was born an illegitimate child but later became legitimized once his parents married five years after his birth.
It is not enough to have a legitimate marriage. One need to make a dynastic marriage. A marriage is dynastic when it is done within the conditions of the House Laws (read: an Ebenbürtige partner).
The second in the line of succession to the headship, Prince Luitpold, legally married Beatrix Wiegand, a lady neither royal nor noble. So this marriage was not dynastic. In 1999, in the twentieth year of this marriage, the Chef of the House (without issue and his brother without issue as well) were confronted with the lack of successors and decided to declare the marriage of Luitpold (both his parents were from the House of Bavaria) dynastic.
By declaring this wedding dynastic, it had consequences for other legal weddings with "commoners" : these were declared as dynastic as well. So yes,since 1999 also Prince Manuel is a dynast and a successor but far down the line:
Franz Prinz bon Bayern, Herzog von Bayern (1933)
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01. Max Prinz von Bayern, Herzog in Bayern (1937)
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02. Luitpold Prinz von Bayern (1951) x Beatrix Wiegand
--. Auguste Prinzessin zu Lippe-Weißenfeld née Prinzessin von Bayern (1979)
--. Alice Prinzessin von Auersperg née Prinzessin von Bayern (1981)
03. Ludwig Prinz von Bayern (1982)
04. Heinrich Prinz von Bayern (1986)
05. Karl Prinz von Bayern (1987)
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06. Florian Prinz von Bayern (1957) - a priest
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07. Wolfgang Prinz von Bayern (1960) x Beatrice Gräfin Lodron-Laterano
08. Tassilo Prinz von Bayern(1992)
09. Richard Prinz von Bayern (1993)
10. Philipp Prinz von Bayern (1996)
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11. Cristoph Prinz von Bayern (1962) x Gudila Gräfin von Plettenberg-Lenhausen
12. Corbinian Prinz von Bayern (1996)
13. Stanislaus Prinz von Bayern (1997)
14. Marcello Prinz von Bayern (1998)
--. Odilia Maria Prinzessin von Bayern (2002)
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15. Leopold Prinz von Bayern (1943) x Ursula Möhlenkamp
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16. MANUEL Prinz von Bayern (1972) x Anna Prinzessin zu Sayn-Wittgenstein
17. Leopold Prinz von Bayern (2007)
--. Alva Prinzessin von Bayern (2010)
18. Gabriel Prinz von Bayern (2015)
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18. Konstantin Prinz von Bayern (1986)
--. Maria del Pilar Prinzessin von Bayern (1978)
--. Maria Felipa Prinzessin von Bayern (1981)
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19. Adalbert Prinz von Bayern (1944) x Sandra Burckhardt
--. Bernadette Désirée Prinzessin von Bayern (1986)
20. Hubertus Prinz von Bayern (1989)