I can only guess that the ever so slight difference in the frame geometry along with maybe how the engine is place in the frame combine to give clearance or not. I was running without gaskets so that wasn't even an issue. I had meant a long time ago to run a bead of RTV under the cover but never did get to it. Since I had most things already apart I pulled both covers and put the RTV on them.I don't think it is the gaskets making the problem, as when the screws are tightened down, my block-off plates contact the valve cover, compressing the gasket. I'm thinking a minute difference in some castings of the valve cover may be to blame. Wouldn't take much to cause interference.
Tim, did you remove the bolt that is just above the carb boot? It looks like it is missing.
I can rest easyer now knowing that mine arent as bad as yours , that 2nd pic looks bad so its good to know that it will still run like that. glad you got it the valve cover back on, I too had to remove the screws from snarfs block off plats, i forgot about that part til you already figured it out..