Oh interesting. I assume it only recommends combining if bagspace will improve (i.e. you have 20+ of a crystallized item, or an existing partial stack of the eternal)?

It combines them as soon as they are enough of them to do so. But actually crystalled shards have a stack size of 10 so it always improves bag space. This is more arguable for Lesser Cosmic Essences but I think you already have combined items most of time.

The count thresholds are stored as values of the ITEMS table.

Yea true, you don't lose any bagspace from the elements, but you might not always gain it. Essences it would be a minor pain, but not a huge deal. I'll get it merged whenever I get a chance, might even add in more items.