Your presentation of the problem simply demonstrates that you're not really looking for a solution. The problem is not black/white, there are shades of gray possible. Including Houdini or other engines doesn't mean that the rating list will suddenly be swamped by a multitude of unknown and anonymous engines.
Some rating lists have actually managed to solve this issue in an intelligent way, see for example Ingo's IPON list, and more recently Frank's SWCR and Sedat's SCCT. Note also the approach of Martin for the TCEC tournaments.
Solutions are surprisingly easy to find when you actually start looking for them...
I think we have to agree to disagree on this.
First up is the dishonesty. Cloners/derivers seldomly admit they are working off another engines code base. They usually postulate that they have writte it themselves and wants full credit/money or whatever. They also don't adhere to the GPL which I believe means their engine is more or less illegal.
Another thing is the testing time which is valuable. I think it is simply a waste of time to test so many nearly identical versions of the same program.
Third is the chaos. Suppose everyone released their own Ippolit engine tomorrow. There is nothing preventing that. Some may have made improvements, some not.
The right way to do it, if you really want to make a very strong engine, is to join forces like they have on the StockFish team. This way the engine is keept to a single branch on the engine tree and everyone gets the credit/money they rightfully deserve.
If you indeed are a lone wolf and can't work in a team then at least be honest about the origins, and let it up to people to decide if they want to include derivatives in their tournaments. This is what happened to Toga and that worked out just fine as I recall.