Reason for kanji and reading in 頂の座 Hecate Character of Shakugan no Shana, Hecate, has a title of 頂の座, which is supposed to be read いただき・の・くら (and is pronounced as such in anime) being translated as "Master/Supreme Throne".
Info about about readings and meanings was checked with / found on Jisho.org

While 座 has similar meanings (seat/place/status/pedestal) and is also used in a compound for throne (王座) it has no reading くら and くら does not mean "a throne" (saddle/warehouse/treasury/contest). That said, there's a word for throne 位 with strikingly similar reading くらい.

Is it a play on something? Is it really switch between 座 and 位 (and would the くらい -> くら change signify something) or just an undocumented reading of 座?
(does not have to be an official explanation)

Maybe maybe even 頂 plays a role here? 頂 also means to "receive" and if くら means a "depository; treasury" maybe it can be a play on the - allegedly she's somewhat different in anime vs manga, but at least in the anime iirc she seemed to be sort of a shell/container (くら) yearning for receiving (頂) experience/emotions? Just a brainstorming
Kura is a valid reading for 座.

Wiktionary stated that it's another kun-reading for 座 which means "high place" as a suffix.


  Readings
  
  
  Kun: すわる (suwaru, 座る, Jōyō); くら (kura, 座); います (imasu, 座す)
  
  
  Affix
  
  座 (hiragana くら, rōmaji kura)
  
  
  high place
  


This also complies with Kotobank, an online Japanese-Japanese dictionary:


  デジタル大辞泉の解説
  
  くら【▽座】
  座る場所、また、物をのせる所。他の語の下に付いて、複合語として用いられる。「天磐座(あまのいわくら)」「高御座(たかみくら)」
  
  
  
  大辞林 第三版の解説
  
  くら【座】
  高く設けられた場所。「天の石座いわくら」「高御座たかみくら」「御手座みてぐら」など、複合語中にのみ用いられる。


Translation:


  Explanation on Digital Daijisen
  
  kura (-座)
  A place to seat, alternatively, a place capable to put a thing. Used in compound words. 天磐座 (amanoiwakura), 高御座 (takamikura)
  
  
  
  Explanation on Daijirin
  
  kura (座)
  A highly established place. 天の石座iwakura 高御座takamikura 御手座mitegura. Only used in compound words.




(For the explanation regarding her name and title, please read кяαzєя's answer)