Actually I wasn't saying anything, just suggesting to play around with settings...
Are you sure that you have Configuration --> Stock --> Allow checkout set to false?
This is the setting that controls the checkout out of stock.
Hardly I find that the mod has anything to do with it, since it calculates totals for all the product variants, if those are exceeded it shouldn't be allowing checkout.
Sorry but unable to help you further, at risk to frustrate you even more I have to tell you that it does work for me.
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