Greetings,

I am the author of Factorissimo3
I have received the following bug report.

https://github.com/notnotmelon/factorissimo-2-notnotmelon/issues/91

It seems in 2.0 RSO does not respect the following codes

if remote.interfaces["RSO"] then -- RSO compatibility
remote.call("RSO", "ignoreSurface", surface_name)
end

Ignoring of surface seems to work correctly but you need to ignore it before you create it.
And currently surface creation event is coming before your ignore surface call:

  29.590 Script @__rso-mod__/control.lua:2003: Creating surface nauvis-factory-floor
  29.590 Script @__rso-mod__/control.lua:2004: nil
  29.594 Script @__rso-mod__/control.lua:1061: Starting area spawn for nauvis-factory-floor
  29.709 Script @__rso-mod__/control.lua:2126: Ignoring surface nauvis-factory-floor
  29.710 Script @__rso-mod__/control.lua:2126: Ignoring surface nauvis-factory-floor
  30.989 Script @__rso-mod__/control.lua:2003: Creating surface factory-travel-surface
  30.990 Script @__rso-mod__/control.lua:2004: {
  ["nauvis-factory-floor"] = true
}

And also factory travel surface is not ignored which will also trigger starting area generation on it.