It seems like there are a lot of interesting experiments to be had here. The lab-play scenarios having a time-related component seems like a good idea, I assume most Factorio players that keep biters on treat them as a combined temporal-spatial constraint, so you have a sort-of proxy comparison to a real game situation when you put the agents on a timer.
I like the way that the framework design is testing different things than micromanagement proficiency, such as what we have seen in DOTA 2 or StarCraft 2 experiments. Notably, severe worker micromanagement (in the case of the latter game) becomes a way to squeak out extra minerals when you have infinite APM available. This is an interesting learned behavior in a narrow context, but that tactic is really control intensive and has a high chance for even pro players to screw it up when attempting to do so. It also doesn't seemingly give additional insight into an agent's longer-term planning, execution, and analytical performance. FLE seems way more interesting as a higher-level "thinking" evaluation framework, with all that in mind.
Any plans for layout optimization benchmarks? As in, start with a given factory cell with X inputs and Y outputs, and optimize its performance.