We use PaperMC for it's stability and performance benefits and expedited plugin updates / support.
It's important to understand that running a pure vanilla server is not as practical as it sounds, primarily on the back-end. The most impactful plugins we use are for server management. We use PaperMC as our server Jar. We are aware of Fabric and the benefits of using it, and may one-day switch to it. But for now we rely on Paper for a lot of reasons. Most notably their reputation for quickly patching game breaking bugs and performance implementations. As well as a vast abundance of user support and documentation which makes running a server much easier.
As a compromise we have toggled as many of PaperMC's "fixes" as possible.
For example, the following unsupported-settings are toggled:
allow-permanent-block-break-exploits: true. (allows breaking bedrock)
allow-piston-duplication: true (allows tnt duplication used in auto farms as well as carpet and rails)
fix-curing-zombie-villager-discount-exploit: false (Meaning villager discount stacking IS possible)
And yet, the usage of PaperMC still somehow infuriates the edgelord collective consciousness...
So here's a message from another server owner regarding the fabric vs paper debate...
"On a technical level, Fabric and Paper are very different. Fabric started as a feasible alternative to Forge, a server running Fabric uses Vanilla as a full source and does little to modify that server code. Paper on the other hand, has been developed from server stability sentiment, as vanilla Minecraft is very unstable under large player loads and large TPS drops are known, aswell the resource consumption would mean high server costs. Next to this, the management and adminsitration of a server using a paperbase means you benefit from server knowledge and plugin development since the days server modding started, which results in mature and well developed mods. This means decent permissions, proper chunk and block backups, done by systems that have been in use by large server providers for years. Next to this, every Fabric mod used will increase the amount of resources used per player, therefor lowering the player cap of the server drasticaly. `Some of the mods that are desired on a fabric server, come build in to the paper server, and use little to no resources per player due to their integrated nature."
To be clear, we're not against Fabric, but in the meantime PaperMC suits our needs best. We've toggled as many settings to vanilla values and un-patched gravity duping. As for some of the more obscure differences such as the differences in redstone behavior, the differences are so obscure that most players will likely never notice, and most farms are designed with spigot/paper in mind anyways.