Pretty much all train companies are vast old overcomolicated state-run monoliths that are very used to everyone working around them in their own country. Such organisations suddenly having to work together with others as equals requires a culture shift. Not to mention the technical challenges, the IT systems - if they even have any, or any from this century - are typically vastly different. They'd have to invest massively in modernisation and standardisation before they can even think of integration. This requires a multi-year effort and a lot of investment, which many states are not ready to make.

Sauce: the Swiss state-run train company SBB/CFF/FFS is and has been working hard to integrate the systems of just our neighbours, and it has been .... interesting.