There is some conflicting information, sometimes with a figure distributed by "Metabolon", wherein the Metabolome is included as the last end in the cascade of the "Central Dogma of Biology"
There are many metabolites which are of pure geochemical origin (e.g. H2O), and many reactions which occur without enzymes (although generally much slower).
In contrast, the existence of complex proteins is strictly bound to the 'central dogma'.
The question is where you stand on that issue? It is pretty clear that FC Crick, did not include (the sum of) metabolites in his Concept of the 'Central Dogma'. Nor did our concept of a metabolite fundamentally change since that time.
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The answer to your question as stated: "Does the proteome really make the metabolome?" is no, not completely. For example RNA is a catalytic molecule, so some metabolites can arise from a non-protein source. I'm sure there are other examples of non-protein catalysis. But the figure above isn't meant to be perfect, is it? For instance, there's no arrow pointing from RNA to DNA, yet the central dogma didn't implode when reverse transcriptase was discovered. When I see a figure labeled "Central Dogma" of anything, I tend to append (in general) to it in my mind.
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Molecules that don't change are not metabolites by definition. I don't quite get what you're asking though.
-> 'to a certain amount unchanged'; The question is if the matter is conflicting to you or clear cut.
I've moved this post to the forum, as open-ended discussion should happen there. ("where [do] you stand on that issue?") Furthermore, if this would evolve into an objective question, it would be a better fit for http://biology.stackexchange.com/