I too have a “low” resting heart rate and the week average with Garmin is usually in the 36-40 range.
I do not think this effects metabolism however because the amount you move is more important than your heart beats for resting metabolism. Otherwise without movement in the equation basic metabolic functions of the body don’t have a huge difference.
One thing to mention that Amber always is so good about is never dieting on the bike, or around training. This is where your body needs extra and will use so as fuel, not for fat. Use zone 2 rides for fasting and getting into a caloric deficit but you are severely under training if otherwise you aren’t feeding.
One common phenomenon is someone who is in a caloric deficit from training subconsciously adapts for it by not moving as much the rest of their day. This will try to equalize the calorie deficit.
I have found better training and weightless when eating more whole foods and carbohydrates to replace what I burnt in a training session. A bowl of oatmeal, a smoothie, etc.
Prior to a training session restore the deficit you have been in with a quick carbohydrate snack like a bar, a sandwich, etc. and feel good about training hard, there will be an opportunity here to get more fit.