boat in a bucket...think boat in a bucket. It doesn't matter if or how fast the bucket is moving, the boat has no idea that a current exists. It has no effect on the boat and it feels no additional forces (unless, of course, it's tied up to something stationary). If there is a breeze from the north and the bucket, with the boat in it, is being carried equally as fast to the east, the boat feels the water to be stationary but the wind from the north east. If the bucket is being carried to the south just as fast, the boat feels no wind. Its our visual perspective that leads us to think the boat feels a difference - I have to shake the notion when I'm in the bucket myself!
A boat that can point higher and sail faster will still be the fastest when sailing upwind into a current - boards or no boards. They're all in the same boat...er...I mean bucket.
As to why you can make better headway upstream when paddling at 45 degrees to the current, I have no idea.