Many subway-trains in Japan are trains for the first 20 stations, then "subways" for the next 10, then trains for the 20 stations after that. Same cars. They may have been 3 separate lines at one time but they got connected.
Also, from a regulatory standpoint, freight and intercity railways (e.g. not subway/light rail/metro/trams) are subject to full FRA regulations, compliance with which would add even more costs, for little real benefit at the speeds they travel at.
Plus, in practice subway/light rail is electrified, and anything else (again with few caveats) is not. In towns with both it is very rare for them to use the same stations.
*There’s probably an exception to the exception for the Akita / Yamagata branches that partially run on regular train lines.
There are few rail networks that manage to serve both well.