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Who knows, maybe the best new features will, as you say, be rolled into the main Reddit site.
Reddit has always been more transparent, and this is just another example of it. On the other hand this is where Digg, and the U.S. political system fail.
As for how non-programmers can participate, I think it is hard to do so w/o knowing how the site internally functions. There needs to be a document available that explains that in simple terms. After that I would guess you just submit a suggestion for consideration by the community.
You are probably right about the voting/social way of testing. I assume they will initiate threads/forums where people can debate the pro's and con's of a particular implementation. What they would probably do is read the conversations and decide for themselves what the best arguments made so far have been and implement those ideas.
The great part about open source is any other programmer can read those very same conversations, make a different decision, go beta, and get more feedback for everyone to absorb. Perhaps his implementation will convert people. The cycle continues.