Early on in my consulting career, I advised a client to use a taxonomy and categorisation system for the community which was distinct from their other content articles and internal structures.
In the short term, this was better for the community. But seven years later, this made it difficult to do really simple things.
For example, if you want related discussions to show up alongside relevant content articles, how will your system know what’s relevant? How will it know what keywords to match? Because I had advised a different taxonomy, there was no metadata to connect the two.
If you want to automatically route relevant articles, know what products members are talking about, or do anything which involves connecting two systems, you have to think through precisely how that will work and plan in advance for it.
Generally speaking, it’s unlikely a company is going to change its entire taxonomy and data structure to suit your community. So if you want the community to integrate with other systems, you need to adapt the community as best as you can to your current systems.