Have there been any rules established for creating NPC stat blocks with class grafts and alternate class features, e.g. an experimental weapon prototype mechanic NPC?
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I don't believe anything like that's been published, but I also think you're fine to go ahead and make whatever substitutions of alternate class features you like for your NPCs. Just to keep thinking simple, it'd be worth thinking about ways to simplify any particularly complicated class features (like how the NPC class graft version of Stellar Alignment involves a bit less tracking than a PC Solarian) though. Depending on the level involved, I think experimental weapon mechanic wouldn't be too bad for an NPC to have, as long as it was used sparingly. Getting +level to damage give experts a bit more teeth, but if every baddie the PCs encounter has that ability...sounds scary :D
Ultimately, NPCs don't need to follow the same rules as PCs.
Let them do whatever you want them to do, just make sure you compare the attack rolls, damage rolls, defenses, etc to other monsters/NPCs so you can correctly identify the CR of the monster you've created/customized.