To treat this with some measure of seriousness:
a) The Chemical Brothers are not affiliated with this website in any official capacity, and therefore aren’t likely to see this, although every couple of promo cycles they decide it’s a good idea to do a fan q&a on here so you could bring it up there if you’re willing to wait around.
b) The people to ask about this would, regardless, probably be Adam Smith and Marcus Lyall, who’ve been responsible for the group’s live visuals since their inception and are given considerable creative freedom w/r/t what sort of imagery and themes appear in them.
c) As a devoted enthusiast of Smith and Lyall’s work, my decidedly non-authoritative opinion would be that the use of medieval Christian imagery is a deliberate subversion of the lineage that “The Private Psychedelic Reel” traces back to traditional Eastern and specifically Indian musical styles, by way of the exoticized and mystical uses those sounds were put towards in the 60’s psychedelic music that “Reel” is more deliberately trying to evoke (and, even more narrowly, the use of sitar in Beatles tracks like “Norwegian Wood” and “Love You To”). Part of the considerable trust the Chems place in their visual team stems from a shared desire to avoid the obvious aesthetic tropes of the 90’s electronica scene they came up in - the sort of instincts that led them to use an archival photo of hitchhikers for the cover of their first album instead of some spiffy CGI rave-flyer imagery. So when the obvious new encore number for their live shows was a transcendent 9-minute piece drenched in sitar, with a snake-charmer clarinet solo dominating the back half, Smith+Lyall’s first creative priority was probably to avoid going
full Astralasia, and to, if possible, find the exact aesthetic opposite of going full Astralasia while still capturing the euphoric, transportive feel those evocations of Indian mysticism in 90’s rave culture were typically meant to elicit. What they decided on, in accordance with their within-technical-limitations approach of rapidly flashing still images, was to swap out Westerners’ appeal to an Eastern higher power with a direct appeal to the archetypical Western higher power, by way of a rapidfire montage of medieval Christian artwork. Even back in 1997, though, they seem to have had some reservations about the message that would send - even if not the exact ones you identify - and so gradually interspersed with those mosaic figures they included
multiple stills of a laughing clown, another visual signifier they’d return to often (both of them, in real life, coming from a lineage of practicing clowns). It’s an attempt, I think, to construct that psychedelic sensibility of images euphorically colliding and some greater voice arising out of the nonsense, but with elements exclusive to their own culture instead of passing the responsibility for transcendence off to some external cultural force. When they revived that version of the visuals from 2016 onward there was a more consistent thematic focus on the religious imagery, but some subversion still creeps in with the “Sympathy For The Devil” interlude where the hallowed images of saints and martyrs are replaced with grinning demons in the exact same crisp, colorful stained-glass style. This didn’t abruptly become a
Hillsong concert.
(Again, though, if you’d like to make an effort at taking this up with Smith or Lyall I doubt they’d take your concerns entirely unseriously. If nothing else they’ve clearly stepped into these aesthetic choices with some measure of deliberateness and could therefore make an effort at explaining them.)