Hi Rick, we managed to do what you are saying. Like you said, MERN is defined perfectly like a starter kit should be and simple enough to separate out the api server. I put up a couple of sample repos which have the code separated out github.com/sudhamab/mern-without-api-server and https://github.com/sudhamab/mern-api-server. These can be run in conjunction and it took very little effort to do this. I think the kit is great in that it lets you keep things simple if you want to or then modify it.
As for the other Universal Hot example you were mentioning, thats really good too and we like it a lot, but it packs in a lot of stuff so initially we got a bit overwhelmed because the reasoning behind how certain things were done were not obvious to us. I think at some point we'll have to learn from both these and create our own version of it. Thanks for mentioning it though.
PS: The credit for the underlying code for the 2 sample repos above has been given to the Hashnode team. I just wanted to share it as an example for reference in case it helps others like us.