This mod is very cool so far, I played around with it in editor mode and have a few thoughts:

Deleting surfaces when there is not enough computation power feels pretty punishing. I had blueprints so could easily reconstruct the vsurface, but if I didn't it would have been pretty annoying.

For the 250M processing unit in 1 hour milestone, is this supposed to be done with one template being ran by many clusters? I compiled a very large template for crafting processing units, near the limit of how many computation arrays I could fit around a MK1 TCC while still compiling the template. It seems like i'll need to make ~10 clusters running this template in order to reach the milestone. This would be fine, but if I set up cluster 1 and then copy/paste it, the new cluster is still set to cluster 1. I'm not sure on the technical details, if this could be a parameter or something and easily assignable to a new cluster name, but it would be nice if we could copy/paste clusters without menu-ing through every entity (there were a lot, this is a big cluster) to set it to the new cluster. Maybe I'm approaching this wrong?

It's also a little tricky to see what is still needed if you are missing a building in the cluster, you check the TCC and it just says Attention Required. Once I made the first cluster it was pretty easy after that, it was just getting the first one set up and working that was tricky from the lack of detail. I read through the tips and mod page a few times and eventually got it working.

I agree that vsurface deletion can be punishing and may force you to load a backup or something. What alternative do you propose?

As for 250M milestone. The intended way is to compile a template for blue circuits. Not extremely large or anything. With output of around 1000 blue circuits per second. Then you will need one cluster executing this template, with at least 70 crafting power (equates to 70 operational normal quality MK1 mainframes). And you need to run it for 1 hour at full capacity.

Honestly, I think that 250M is doable without virtualization. The script that unlocks the research checks the production statistics (sum for all surfaces). So you can just produce the equivalent of ~290 4x stacked green belts of blue circuits for 1 hour anywhere.

That makes a lot more sense now, I didn't realize you should use multiple virt mainframes so I was looking at scaling clusters instead of scaling those. For the vsurface deletion, after playing some more I think they are fine as temporary surfaces. Like you said, a save reload would easily step around it, I was just surprised.

A possible alternative could be to set every entity inside the surface to https://lua-api.factorio.com/latest/classes/LuaEntity.html#disabled_by_script. But I'm not sure if that works, I've yet to play with this mod.