Remember that some users are in early phases of a staging site and may want to test out a mobile-first approach. Not everyone designs everything in Figma early on and in some cases design as they go. Whether that’s best practices or not is another matter, the fact is it happens with many freelancers 
There’s two things here:
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If this behaviour is caused by what you suggest it is, then I think while this is likely rare, any typical user would consider this a defect/bug. There is a “reset” button in the custom breakpoints dialogue box, a user would understandably expect that the reset button puts things back to how they were configured. This means that any “mobile-first” logic would go back to “desktop-first” logic. If the reset button doesn’t actually remove mobile-first specific settings, then it seems like a gap/bug in the functionality of the custom breakpoints. For the Academy, I suggest this either go under “known issues” or on the page you linked to at least make it clearer that it will ruin a site in a way that is not reversible - that’s a very large impacting behaviour if it’s caused by what you said and should be better emphasized in my opinion.
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But as I later determined and posted in a newer post, you’ll find that this actually appears to be a defect specific to 1.8-beta and not related to what you originally described as the root cause (mobile-first breakpoints) since I can reproduce this behaviour without even touching the breakpoints on a fresh site and simply installing a fresh 1.8-beta release.