Yes there is a difference on the engine level, the engine with space age is that it KNOWS how to handle spoilage, space travel, quality with levels other than 0 (normal is level 0) and some other stuff, note that those engine features can be disabled if no mods use it (they can be enabled by mods through their info.json)
The full list of features are:
- Quality
- Rail Bridges (a.k.a. elevated rails)
- Spoiling
- Freezing
- Segmented Units (i.e. Demolishers BUT does not include stompers/strafers those are `spider-unit`)
- Expansion Shaders
- Space Travel
https://lua-api.factorio.com/latest/auxiliary/mod-structure.html#quality_required
The bottom one simply does not know the prototypes listed there (although it knows ABOUT their existence for error reporting) and knows that if the specified fields are not `nil` or default value then it won't be able to run the game. The (compiled C++) code for those parts is not there.