The assigning of markers to clusters does not really happen at the R side of a leaflet map, but on the javascript side; all that {leaflet} does is "only" passing the options.
You will find some documentation on https://github.com/Leaflet/Leaflet.markercluster#defaults - the interesting part seems to happen at maxClusterRadius - this defaults to 80 pixels, with option to override. So you should - in theory - be able to achieve smaller (denser) clusters or larger (more sparse) ones by tweaking this parameter.