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However, at the same time, many of the so call proofs accepted for things like dice games could be cooked by a skilled programmer.
Only if the hash function behind it is broken. The basic principle that makes the rolls (not the site !) proveably fair is that the server can provide a hash of the seed used to generate the rolls. Once the full seed (or the servers part) has been revealed the player can check that its indeed the correct seed and that the rolls had to be like this.
Open source isn't a protection either as it may not be the actual source for the program running. There are many backdoors. However that type of exploit takes a lot more skill than a Ponzi operator stacking the deck. The counter point is I don't see how any gambling game can be really made provable fair.
It is of course still possible that the operator of a site itself is not honest and runs with the wallet (e.g. dice.ninja), but this is true for all Bitcoin services that do not work directly on the blockchain. Even those running directly on the blockchain coud run, at least with parts of the funds, by stalling the payout for a bit.
Thanks, Ill drop in