Generally, kids with IBD do better with formula - it is absorbed much more easily. Is he in remission (shown by scopes)? That is different from symptom free.
That said, my daughter was put on calcium citrate and vitamin D in addition to formula when her first Dexa scan came back low. But until she was a healthy weight and was able to maintain that weight, she stayed on formula. She has only very recently taken a break from tube feeds.
My daughter's Z scores were definitely not as low as your son's and we were sent to a nutritionist ASAP. Her GI was very concerned.
Many GIs like kids to stay on formula to help with growth and weight gain, even when they're in remission. Bone density continues to increase till the early 20s, and then it stops, so it's important to increase his bone density now.
Weight bearing exercises also help. Unfortunately, the usual exercises for kids with arthritis - low impact, things like swimming and biking - do not help with bone density. But walking does.
For kids with arthritis, sometimes inflammation can also decrease bone density. Here is an article about that:
https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3043287/
Some studies show that anti-TNFs can increase bone density in kiddos with arthritis. Has your son started Remicade yet?
I would check with your GI on specific instructions.