Watching Direwolf20's videos, I know the smartypants mod developers on ForgeCraft all have a set of six crystal clusters (one for each primal aspect) above their research tables, and The Great Azanor His Ownself (the Infusion Altar earned him that five-capital nickname) plays there and discusses mechanics. So I suspect what they're doing is the right way.
I can also confirm from my own experience, albeit circumstantially: I had a ton of trouble finding Fire Shards in my playthrough, so I have crystal clusters for every primal aspect
except Fire near my research table, and my research table has stars on every primal aspect except Ignis. However, I don't have a source of Fire near my table, so it remains possible that other things are determining these research bonuses (though it's hard to think what would have given me an Order or Entropy star).
As a test, I just knocked down my Air Cluster to see if that would change anything. The star on Aer didn't disappear immediately (even after a relog), so maybe there's a delay, or maybe a star remains until it's used up... or maybe crystal clusters
isn't the whole story, despite all the evidence above.
I'm also going to see if adding a mixed cluster will give me that Ignis star---I still don't have enough damnable fire shards!