Whenever I've flown from Havana through Miami to transfer another US flight (us citizen), I see everyone goes toward the same customs area, then US citizens follow one sign and non follow another. Since I'm transferring flights after customs, I go to baggage claim, get bag, re-check bag, and go back through security. At some point after customs I usually see Cuban families waiting outside the exit door and greeting their loved ones who just arrived. So I think everyone's shepherded through the same areas for international arrivals, albeit to different counters.
I've done this 3 times now and generally it takes AWHILE even though I have Global Entry so my customs is super quick. I usually leave 3+ hours between flights and don't have a ton of time to spare. There's always potential it can go faster but Miami airport can be really crowded and dysfunctional so better to be safe.