I think when you have a number of conditions it can be difficult to work out what is causing what sometimes. I've got hypermobility and there is EDS in the family. I am very flexible, things like you said you can do, though the rheumatoid arthritis makes me less and less flexible as things go on and I have fibromyalgia too and orthopaedic issues with my knees so it's all a bit of a mixture!
If I remember right, you have arthritis associated with your IBD? Do you see a rheumatologist for that? It was rheumatology who diagnosed me with the hypermobility.
They could also maybe help with a referral to physio (if you don't already go) who could help you with strengthening exercises and mobility aids. I'm currently working with them to help strengthen my core and muscles round my joints to help stabilise them.
Some conditions do tend to run together, I have some intolerances and allergies and have been investigated for IBD, have asthma and some eczema. I think that, especially in autoimmune things, that your immune system just makes you more prone to things, though things like asthma, eczema and some intolerances are quite common generally. It's hard to know.