With FME Flow, you can license as many or as few engines as you would like, although there are some services which will always use a single engine such as Streams.
In your scenario, you would only ever need one FME Flow license and likely one ArcGIS Server license (Contact your Esri representative to confirm).
If you had for example 16 workflows all connecting to ArcGIS Server, and you have 16 FME Flow Engines licensed, your 16 workflows could all run simultaneously. If you only have one FME Flow Core, those 16 jobs would run consecutively through a queue until all jobs are completed.