If I understand you correctly, that would mean you cannot backup your config files by making a copy of /etc - you would end up with a bunch of symlinks instead of the data itself.
In that case, I prefer the standard way of doing things. The names could have be chosen better and the difference between the purpose of some directories is sometimes not clear, but I like how it separates static data (binaries, documentation) from configuration and from other variable data and from user data.
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