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I suppose alterations could be made to Steam's achievement system to allow achievements to be half-unlocked if done under house-rules as opposed to standard-rules (appearing as a different color, an asterisk, or something until you unlock it again w/ standard rules.) But if you're not happy with non-unlocks I don't think imagine you'll be happy with half-unlocks.
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Ideally that shouldn't be even accidentally misleading. This isn't designed to be punishment to modders by exclusion - it's designed to communicate certain contexts clearly with whoever is browsing your profile.
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If someone sees you have a certain achievement, they'll assume it's because you achieved something in the game that is being sold as opposed to a house rules version of it. I voted against because achievements are understood, as a system, to be something that is applied to the standard-issue main game.
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