Well, bone desnity is just one example of something a person cannot change about their own body that does affect metabolism.
I gave another example of lung capacity. A person can train and increase their lung capacity. That does not mean they will have the capability to become the next Michael Phelps or Lance Armstrong (even if Armstrong did cheat.)
The point is, everyone's body is different. You can change the physiology of your own body to some degree (and it can be quite drastic). But you cannot change it to be or act just like another person's. That point, somehow, was completely lost on a few people.
There are biological reasons for variation in weight and susceptibility for obesity, but again, bone density is not one of them.
Bone is metabolically active and remodels itself due to various stressors, one of them being weight. The more weight you have, the greater your bone density, so again, overweight people will have greater bone density and by your faulty hypothesis, a higher metabolism (which they do because of their greater mass to maintain).
As well, the whole old wives tale of 'big bones' really doesn't hold any water as the difference in weight appears to be minimal (see the bolded below).
This has been well researched due to the almost epidemic osteoporosis in elderly women, so there is a lot of research on this topic.
We have done bone density scans on loads and loads of people to know this.
http://jn.nutrition.org/content/136/6/1453.full
Bone, Body Weight, and Weight Reduction: What Are the Concerns?1,2
A low body weight is associated with low bone mass (1) and an increased risk of fractures (2), whereas obesity is associated with increased bone mass (3) and reduced bone turnover (4,5) and loss (6,7).
Although the additional bone mass in obese compared with lean subjects contributes only ∼0.5 kg of total body weight or 1% of body weight (5), it is ∼20% of total bone mineral content, thus making a substantial contribution to the higher risk of osteoporosis in lean compared with obese subjects.
I bet it wouldn't take much digging to find bigger/overweight people have a greater lung capacity as well.
I would recommend you look more towards genetic polymorphisms, like GLP-2, ghrelin, leptin...........