|Problems? Is your data what you think it is?|
I would like to recommend to let the author decide whether or not a piece of code should be highlighted (i.e. not make it configurable in the User Settings).
I think you raise a good point but I think that you need to consider this idea more carefully from more angles.
For example, I don't care what you or any other author decides, I don't ever want to see rainbow code (at PerlMonks when I'm logged in). So it needs to be a choice of the viewing user. You make a good point about there being value in it also being a choice of the author.
However, I don't care what burden you hope to put upon authors about declaring what type of code they have posted nor hoping they will check whether the syntax highlighting is doing a good job on their code; I won't be shouldering that burden for chunks of code that I post and I don't think it is reasonable to expect all authors to (and trying to do that would be doomed to failure anyway, IMHO).
But the more I consider this idea, the more I think it is doomed. Perl syntax highlighting imperfect (always, at this point) and so it is a reasonable option to select to follow for your own code. However, trying to get some other person to bend to the idiosyncracies of the Perl code highlighter that somebody else chose will always just be aggrevating, even unacceptable to some people. This will just be another source of strife.
So the choice of the highlighter needs to be in the control of the viewing user and the viewer needs to be able to disable it when it fails.