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After placing down the following blueprint:
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I cannot manually build the rails correctly: When placing the cursor over a rail and clicking the green arrow, the resulting rails are misaligned with the ghost rails. Bots construct it normally though.
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Thanks for the report. Those are legacy rails and as such the game does not let you manually build them. They exist only to load 1.1 saves and by chance robots can also build them. All future rails you build will be the new ones.

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This is a simpler diagonal-only blueprint to trigger this. Here it only happened to this diagonal track BP with the (absolute) alignment of 4 set. I tried to change the alignment to 0 and 2, but those behaved normally; align=4 and they're offset by 1 tile Again: you can't manually place down rails that would connect to it. That is the frustrating part. They exist, they kinda work, until you notice the strangeness. At that point you are forced to tear down those rails or spaghetti onto straight segments only.

I think this will cause more issues and reports later as people begin to mix rails from old books in new worlds.

This blueprint came from another player online on a fresh 2.0 map and I persuaded them to share it with me. Since Factorio 2.0 converted it to "legacy-...rail" I couldn't retest it in an older version, but in 1.1.110 alignment doesn't cause issues. While it is nice that the rails continue to work and blueprints too, I'm afraid it's gonna cause more issues down the line.