Title sums it up, but I'll break it down into two parts.
Part 1: Will console commands disable achievements in Steam?
Part 2: If achievements are disabled will it be forever or just for game session?
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I'm going to say they probably don't.
I think this because Bethesda plans to bring mods to all platforms, and some will need access to some of the 'cheat' commands.
A good example from Skyrim is the 'showracemenu' command, without TGM it would wipe your levels and perks out, some people are going to build benign mods that need that functionality. Now consoles may have issues because mods will probably need to be greenlit before they are pushed out, which would allow them to be tagged as cheat mods.