The 3rd Imperium
--The rise of Cleon Zhunastu (Cleon I), and the Federation of Sylea becoming the new Imperium was no accident of greatness. With the defeat of the Kingdom of Chanestin & the Interstellar Confederacy, and securing the Vland & the Vilani's security & cultural concerns to spinward, Cleon I set about annexing the adjoining states and worlds. While he was innovative and creative, he was also decisive, and declared Sylean year 651 to be Year 0 of the new age. He recreated the Grand Senate, thereby falling in line with the formation of such a body as the preceeding Imperium's had.
But where the former two powers had stumbled and erred, Cleon changed things--namely in year 17 defining by edict "that any sentient being dwelling within the Imperium's borders was a citizen (with all the rights thereof) no matter their origin." This new movement known as Pan-Sophontism while overlooked often in the economic and Imperial might of the military the 3rd Imperium's early rise, was actually a cornerstone of hope and change from the previous empires for the alien sentient races within its boundaries.
The remnant Terran and Vilani faiths that had survived in Vland, Antares, and Amdukan sectors, as well as those in the Core sector around Sylea (Capital) followed along, many of them wrestling with the Humaniti-within issue of Sentient alien Imperial citizens, even as they followed behind the advancing Imperial fleets and trade ships, dealing with the Long Night heresies as they found them.
The peaceful religion of the CoSD-A & Ps sects were horrified by the barbarism their faith had succumbed to warring upon their bretheren, and declared these worlds off limits and heretics. The 2GRC faith, in the wake of Cleon I's announcement began the Third reform--that of proselytizing aliens, such as the Vargr, which the CoSD-A had already done to some extent during the Long Night; the CoSD-Ps followed their parent faith in good order. His heir Artemsus I would initiate & complete the 'Pacification Campaigns' (years 76-120) that gained the 3rd Imperium much of its initial growth; Many of the Anti-Stellar brotherhood CoSD heretical churches were 'liberated' from their warring sins, as the CoSD-A & Ps stood by and let the Imperial Navy and Marines smash their ships and armies, and then restored the true faith back after they were subdued militarily.
The major Terran faiths dealt with their heresies differently of course--where entire planets--(often high median to High population: pop 8-A) had changed doctrine they were isolated, and the smaller world's faithful were absorbed back into the fold. Uncovered in the Imperial wave of expansion, the separate faith of the Unity of God church that had successfully amalgamated the major three monotheisms in several pocket empires that lay between the former Confederation of Terra and the 3rd Imperium. This faith, without prompting, had already brought in sentient alien worshippers.
The Solomani Confederation too encountered the changes the Long Night had wrought in their faiths across the stars as they knit themselves back together, and dealt with them accordingly--sometimes peacefully, other times more stringent methods were applied. The collisions of the Pan-Sophontist movement of the 3rd Imperium however had ramifications with their relationship with the Solomani region however, troubles that transcended faith, and dwelt in the politics as well.
The 2GRC, and other major faiths of the region for the most part, balked at allowing in non-human sentient worshippers, much less allow them into the priesthoods. Buddhism, Shintoism, Taoism however were less affected by this conflict. The Protestant faiths that had changed over the Long Night however, did as their ancestors had done rather than convert or be subsumed into the fold of their parent-faiths, joined those heading out to settle the new frontier region of Deneb, Trojan Reaches, the Reft, and the Spinward Marches.
But with them also went the major faiths as well, though in the colonial era between the 400's to the 700's in the Marches the latter's ability to sway and absorb the splinter sects and cults, or denominations who felt uncomfortable in the -re-expansion of the new Imperium was lessened. Politically most faiths stood outside of planetary politics, save for notable examples such as Deneb, Lintl, Pysadi, Pavabid, Goertel, Simak, Tlazteotl, and a handful of other worlds. One of the major reasons for these worlds high-law levels exist is of course most of them have no wish for the influences of the other major faiths to sway their flock/populations.
The political divisions caused between the 3GRC and 2GRC came to a head behind the scenes in the Solomani Rim war (990-1002). Those 2GRC churches within what had been called 'the Solomani sphere' region of course aided and abetted the Solomani Confederation's efforts to seize back these worlds and break off from the 3rd Imperium, capitalizing on the post 3rd Frontier War chaos, humiliating peace, and the abdication of Emperor Styryx I. Of note within the major faiths, the 2GRC church of Deneb Sector remained loyal to the 3rd Imperium. Scholars speculate even today whether this was due to the nearby threats of the Vargr and/or the Zhodani, or part of the Domain's nationalism for the Imperium in and of itself.
The Solomani were defeated, and those 2GRC churches were replaced as they too fled a possibly vindictive 3rd Imperial Navy that marched to Terra, and retook it by 3GRC clergymen. the wiser of the major faiths in the reconquered region remained outside the fray, and survived unscathed.
The Imperium of 1105 is far from perfect, pan-sophontism is indelibly etched into most Imperial member world societies, and yes, even their faiths to some extent--the exceptions being the one-system theocracies.
finis
--this is my historical analysis of religions through the 1st-3rd Imperiums. It is macro-scaled, and many finer details are of course intentionally missing, for GM's & players alike to make what they will of it. Your comments gentleman of the boards?