Check "XML/Civilizations/CIV4LeaderHeadInfos.xml" to see if theres any mention of a relation bonus for favorite religion.
I just went and compared Alexander's Warlords XML to his BTS XML. These were added:
<iEspionageWeight>100</iEspionageWeight>
<FavoriteReligion>NONE</FavoriteReligion>
<MemoryType>MEMORY_VOTED_AGAINST_US</MemoryType>
<iMemoryRand>20</iMemoryRand>
<MemoryType>MEMORY_VOTED_FOR_US</MemoryType>
<iMemoryRand>20</iMemoryRand>
<MemoryType>MEMORY_EVENT_GOOD_TO_US</MemoryType>
<iMemoryRand>50</iMemoryRand>
<MemoryType>MEMORY_EVENT_BAD_TO_US</MemoryType>
<iMemoryRand>50</iMemoryRand>
<MemoryType>MEMORY_VOTED_AGAINST_US</MemoryType>
<iMemoryAttitudePercent>-200</iMemoryAttitudePercent>
<MemoryType>MEMORY_VOTED_FOR_US</MemoryType>
<iMemoryAttitudePercent>200</iMemoryAttitudePercent>
<MemoryType>MEMORY_EVENT_GOOD_TO_US</MemoryType>
<iMemoryAttitudePercent>100</iMemoryAttitudePercent>
<MemoryType>MEMORY_EVENT_BAD_TO_US</MemoryType>
<iMemoryAttitudePercent>-100</iMemoryAttitudePercent>
<MemoryType>MEMORY_LIBERATED_CITIES</MemoryType> <iMemoryAttitudePercent>150</iMemoryAttitudePercent>
So no, I don't think so.
Hang on a second - I have a sudden desire to check Stalin's espionage weight