I am also on Metformin (for PCOS, not insulin resistance). When I first started taking it caused tons of digestion-related (and other) side effects. I guess my body adjusted because the effects became much less over time. They completely went away when I cut grains and processed foods out of my diet. I don't count calories anymore, so I can't help you there.

It is 100% truth that a caloric deficit must occur for fat loss to occur. However, my own observations show that someone who is overweight can typically eat instinctively and lose weight as long as they keep their carbs low without thinking in terms of calories. This is because eating carbs simply causes many people to overeat. The science is not well understood (but conflicting theories are out there regarding why this really works), but it certainly appears to be the case for most people.

So with that being said, as you approach a lean state, it seems carb restriction alone is no longer enough and restriction needs to be tightened for the last couple pounds. That might be restricting the low-carb foods you tend to eat too much of, or even restricting calories. I tend to consider restricting calories as a last resort because I think it is about the most unnatural and tedious way to maintain good health and weight.

Oh and restricting calories is not a license to eat as much fat as possible otherwise you will gain weight. Eat enough to be satisfied and that's it.