I don't think those bottles have been altered in anyway, a lot of standard glass bottles will have imperfections in them that look like that, amplified by the thickness of the bottle itself. You don't see this with jars because they tend to be thinner than bottles.

The rubik's cube inside a bottle is a fairly easy one, if you've ever seen a disassembled rubik's cube then you will clearly see that it's possible to just feed each piece in one at a time and put it back together with some tweezers and a lot of patience.