I've been using a non-HR Fitbit for 3.5 years and find the calorie burn numbers to be accurate. Fitbit uses the Mifflin St Jeor equation for calorie calculation. Try experimenting with the calculator here:
http://www.calculator.net/calorie-calculator.html
My BMR is 1091 (skinny female)
Sedentary (ie resting): 1309 and
Moderately active: 1691
The moderately active 1691 is almost the same as my Watch 1658 'resting' cals, whilst my Fitbit average TOTAL calorie burn for last 30 days is 1690. I do an average 12k steps daily, Watch and Fitbit are fairly close.
On the Health app Resting Calories are described as 'an estimate of your basal metabolic rate (BMR) [...]' Then why don't they call them BMR?!
So Watch 'resting' calories should be BMR but are more like BMR x 1.5 - moderate activity already included - and then the Activity calories are added on.
Really don't get how they got this so wrong. It's not that difficult, you start with BMR. Then you add the Activity picked up by the Watch to it.
I believe you have hit the nail on the head here. Apple apparently is incorrectly adjusting the BMR by an activity level factor. If we all entered an activity level as "sedentary," the BMR would be correct. The problem is that I don't know how to change that initial activity level.