I did a valve cover placement (Crown Automotive) in the spring 2024 and encountered these exact issues. On top of the fact that the cover holes were "off", the holes in the cork gasket were also way "off." The cover and the gasket are a system and have to work together, otherwise... leaks. Misaligned holes lead to crooked bolts and it jus won't seat right. At least with cork gasket, I was able to trim out where I needed without compromising the sealing integrity. Some holes in the gasket became rather elongated. I have no idea how any of this would work with a silicone gasket.
I spent a lot of time checking the cover and cork gasket fitment "DRY" for alignment. Then I spent more time measuring and checking the bolts and hole depths "DRY". Clean the holes thoroughly with brake clean and chase with a tap if it's full of junk. The front and rear holes on mine were very deep in the head, no issues. The passenger side holes were not, and I needed a little math to make sure that I didn't bottom out the bolt based on the cover and gasket thickness. I did end up using Spankrjs suggestion of metric washers, and that worked so that I was able to still compress the gasket. The driver's side head bolt holes (if you have them) are generally deeper, but you have to check again that you don't bottom out before compressing the gasket. I also used NAPA aviation sealant, and so far no leaks.
I wasn't a big fan of cork gaskets until I did this cover. To me, it was more forgiving for the idiosyncrasies of my head. For information, the previous gaskets was just silicone or RTV. It never really formed around the cover like it should of. It was thin in spots, and didn't stick at all in others.