Looks like the front bolt is safely above the deck. I bet you could even grind a bit of a channel or groove into the sides for the other two. The mast partners (the opening) has some serious extra laminate in my DS1 and I would expect/hope that this is the case for you as well. It's not going to fall over an play dead with a bit of a groove.
And, yes, you are correct that tapped screws like this are probably overkill, and you might as well just rivet. The rivets only prevent the tabernacle from falling off when the mast isn't installed. I don't think they contribute anything to supporting the compression loads. That's done by resting the tabernacle casting on the mast profile...
So, this may even be a non-problem. However, if you find that your boom is too low, or that you can't raise your main as high or your turnbuckles have reached the end of their adjustment without creating enough tension, you can always dig out this thread and start over
Good luck