The fine line between academic research and applied industry research?
My own experience suggests that the academic value can be quite orthogonal to the needs of the business. The company wants to build a product and "ideas" are secondary to that. For the academic, the ideas are at the front. But the work to build and refine the product often gives a researcher ideas that can be developed independent of the product development. Time constraints may require that exploration of those ideas needs to be delayed, but in most cases they can be developed. 

You already suggest one such idea in your question. Keep that idea in your research notebook and develop it as time permits. You may need to abstract it a bit for confidentiality reasons, but you probably want to abstract it in any case to make it more interesting and more general. 

There is no real conflict other than time, assuming that you can present the problems in a sufficiently abstract way that you don't infringe your contractual obligations. 

Spin Off is a big idea. The formal project is a "mine" for ideas. Dig them out.