I don't know if this would be considered working as intended re: diplo ai, but i'm into the early industrial on 4-17, I fought a single 1500 year war against carthage through part of ancient and classical era, and have otherwise been pretty good to all AI's, often agreeing to gift deals and deliberately avoiding settling in controversial regions (including a 4-iron-and-multiple-bonus-resource-tundra location that no one wants to claim). Anyway the war was well justified... carthage forward settled my capital with two separate 3 distance cities, and did same to one of my already-densely packed satellites, despite relatively poor resource locations for each of their choices (they were critical naval access locations though, so no worries about the AI decision making itself)... I acquiesced to this cuz i had no plans for those locations, and had already claimed the important tiles nearby, and most importantly dido had already spread her religion throughout the continent, leaving me and maya (other religion founder) as minority followers of the only regional alternative. Despite religious differences i was friends with everyone early on... but then dido (the early runaway overall) attacked my best buds maya...
The war AI performed admirably in the long drawn out war that followed, at times inflicted surprising losses, but I had a strong progress tech and building pace going and was able to outpace war weariness and eventually overwhelmed dido's defenses. in the meantime, all the other followers of carthage's religion became less friendly towards me, and maya had lost 2 of 4 cities to dido, all of its army, and its capital was down to half health. Initially I had had to focus on the forward settlements due to the strategic obstructions they posed, razing all of them and liberating 2-3 maya workers as i went. My best buds maya loved me even more despite the hardship they faced. I arrived just in time to save their capital, then went on to liberate their other two cities, though it wasn't quick work with all of these on the coast and many recaptures.
Finally, over a millenia later, the mayans saved and hostile encroachments eliminated, I marched on dido's capital/holy city. After hundreds of years more of siege there, I captured it, and instantly turned my world upside down... as the new 'founder' of carthage's religion, the rest of the continent now loved me again, and pacal immediately ended our long-standing bromance with little explanation. A short while later he denounced me... me, the savior of mayan sovereignty! Didn't matter that the same turn I captured carthage, I had an inquisitor ready and eradicated the religion entirely from my newly joined populace (I also cleansed the other minority followers in my cities on same turn). After rebuilding some faith, I also converted my now-vassal dido's other cities to maya's religion, and over a long time with its opposition neutralized, maya was able to turn the tide throughout the continent. Though I enjoyed the diplo benefit from the followers of carthage's religion early on after its capture, now that most of the others have changed religions, I am the continental pariah, unable to make friends with anyone, despite not one follower of this state religion anywhere in my cities. Also, carthage itself has become a forever-starving 1-citizen city no matter what I do, though my relationship with dido has improved sufficiently that I'll be returning it to her soon.
Anyway, TLDR would be nice to have a reprieve from religious diplo penalties if there are no followers anywhere in our civ of the religion we're falsely alleged to be the founder of