Forge Version: forge-1.12.2-14.23.5.2847-universal
Quark Version: Quark-r1.6-179.jar
Log: I would've included this had I read the instructions to include it before I deleted all the server files to restore from an older backup. Sorry.

This config option doesn't work:
B:"Enable Anti-Overlap"=true

For this mod:
https://www.curseforge.com/minecraft/mc-mods/future-minecraft
Which aims to add many 1.13+ features. For example, Prismarine stairs.

When I logged onto server and viewed items in creative mode, it listed prismarine stairs for both Quark and Future Minecraft. Quark also offers "Polished stone" and Future Minecraft offers "Smooth Stone", both look like the exact same item.

For this situation it doesn't matter because Future Minecraft ended up having too many broken features. However, if they do end up fixing it or for other mods, it'd be nice if the config option worked.

Please note that I probably won't check this post again.

Technically this is more of a "missing feature", primarily on Future MC's end rather than on Quark's end. Since Future MC is a mod dedicated to a more specific purpose of back-porting features from newer versions, whereas Quark is a mod dedicated to a more general purpose of expanding vanilla-style content, it's most likely up to Future MC to handle the missing compatibility.

Future MC has an config option to disable its changes to "Smooth Stone" (which is actually a vanilla block that has been in Minecraft since well before 1.12.2), but has no such option to disable its Prismarine Stairs, so "wants" to win this minor conflict by default. The easiest fix would be for Future MC to add a config option to toggle its own variant.

Quark has an option to avoid overlap with known culprits, but must be explicitly designed to handle each case as it comes up -- it isn't an heuristic system that checks for identical names or graphics or anything like that, as humans would reckon. It simply does an on-or-off based on the presence of another mod, occasionally with slightly more logic and sophistication but nowhere near the human level of intelligence. This is actually a good thing, because if it went through the entire object database of every tile and entity in the game to see if it would result in human-recognisable duplication, it'd add at least a few minutes to your load time. =)

Personally, I love both Future MC and Quark! I'm not sure what other problems you're having, but most of them are easily forgiven by disabling them and using the original mods that the vanilla/future versions were meant to imitate (e.g., bees are a mishmash of Forestry's bees' design and Pam's Harvestcraft bees' simplicity, and Forestry's bees and the many bee expansions (Magic Bees, New Age Bee Breeding, etc.) are far more sophisticated and fun than vanilla bees =)).

Ah okay, thank you for your feedback. Strangely Future MC did not have a config file generated. I reported the issue to the developer & removed the mod. I think I'll hold off on reinstalling until the bugs are solved with more updated versions. Things like the blast furnace and smoker didn't work. A large portion I tested was broken, actually. Not sure if it was just that version or maybe a mod conflict, idk. No errors in console from it if I recall correctly.

Also I appreciate the suggestions for alternative / more in-depth mods!