There shouldn't be any difference in runtime operation or configuration aside from the server headers being different. That can trip up CI systems and other tests, but should be easy to update.
The only real differences are in planning and building:
* When you build from source or user a linux distro's binary, the default modules built by OpenResty may not match the default modules built by nginx. You should review your nginx build notes, or what the linux package maintainers build with, and then do the same for OpenResty.
* OpenResty releases are often slightly behind the Nginx release they patch, so you need to ensure any newer features you rely on from Nginx are in the currently available OpenResty version.