This depends on if the samples have their pitch detected and embedded within them or not or if the CODM file presumes they are tuned to concert pitch (A=440). I am not sure if all instruments of Sonus Paradisi use embedded pitch in the samples or not, however you would need to contact Jiri to be sure what the difference is between the instruments you mentioned. If the pitch is embedded then Hauptwerk will be able to re-pitch them all the same when you choose any temperament other than original organ tuning.
The CODM settings applicable to pitch are in the Rank table:
(If samples are tuned to equal temperament)
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<Samples_RankBasePitch64ftHarmNumIfAssumedTunedToConcertPitch>0</Samples_RankBasePitch64ftHarmNumIfAssumedTunedToConcertPitch>
and
(If samples are kept at their original tuning and pitch data is embedded)
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<Pitch_RankBaseOutputPitch64ftHarmonicNum>8</Pitch_RankBaseOutputPitch64ftHarmonicNum>