If you lowered the spell slot by applying it, I could see it breaking something with metamagic stacking. As it stands though, it's a straight nerf for practical reasons and doesn't seem to allow for any exploits. "Doing worse" while not getting below the minimum possible result is still not low enough to create weird interactions(like, say, causing a cure spell to cure negative HP by reducing it further). I'd say keep an eye out for any other homebrew rules because those are the harder to predict, such as an effect that reduces the amount of [anything] by a fixed value or by character level without a clear low cap at zero.