Extensions Recycling and Refining are pretty all compassing extensions covering a very wide range of civilian activities. They are also comparatively low complexity. For example factory skills get multiple extensions just for speed etc.
An idea to improve on the situation: have each commodity or commodity group have a separate extension affecting its refining rate. So you woudl have things like "Refining: Titanium", "Refining: Plasteosine" or "Refining: Nuimqul commodity". This would make it more meaningful how the ore lines go in slightly different places when compared to commodity lines. This would make it interesting on whether you keep your options open to mine and refine whatever is the cheapest at the time or do you "division of labour" it and stick to spesific one be a market leader/competent in it and buy the others.
The situation could be similar than it is now in ore collection where going blanketing all types to lvl 10 would be kinda intensive ep use but it is quite easy to pciak couple to go to a high level.
However with the current on/off system you either refine or you don't. Getting refining for one commodity is as expensive as getting it for all or them.
The is also one reason why the existence of the whole refining step has been called into question from time to time. Before people decide what modules they woudl like to have in ore form instead of in commodity form. I think the main reason is that refinign is instant and infinite capacity. that is I can have gigaUs of liquits and HDT and turn them ALL, INSTANTLY into cryoperine. Now the factory process doesn't suffer from this as its a temporally extended process. I can kinda guess on reasons why that system is not copied verbatim to refining. That is a new player would be disappointed they they have to wait yet another wait before they can get a payoff and that the process is too abstract in going from "thingy called X" into "thingy called Y" taht it can seem like not an essential action.
I would say that make the refining process differetn fromt he factory process int he same way that perpetuum ep system is different from eves skillpoint system. That is an agent or a agent-terminal pair generates over time "refinement" that can be in an instant be used to turn ores into commodities. But the difference to how it now works is that when working with large amount one could run out of "refinement", if you would mine and refine in the go ore as you collect it in argano or sequer loads it would be equally "instant". But if you would do it in scarab loads you would have to break it into multiple pieces or make it in a temporally extended process.
Now you could then add extensions for: how big of a pool of "refinement" you can accumulate before it slows/stops accumulating. The rate of regeneration for "refinement". And possibly even how much a (spesific) commodity eats this "refinement" resource. This would be comparable to the numerous "factory: time efficiency" extensions.
With these it could be an interesting problem on whether you refine quickly and inefficiently or refine into stock in order to not get hit by refinement need bottlenecks. It would also decouple the prices of ores from the commodities more strongly while making them influence one another. It would allow for there to be more niches fillable quicker by relative noobs and less a simple "I have more step aside" single scalar thing.
It does add complexity and it calls for (partial) redesign of somewaht core economic mechanics. But I do think this do not have a high chance ot make unforeseen negative effects nor would they be that tricky to implement.