I took Factorio Space Age (standalone copy, downloaded from factorio.com), starting with no mods. I added PyBlock (allowing ingame mod manager to add dependencies) and did nothing else.

On launch, I get the following message:

The Space Age mod is not currently compatible with Pyanodons. Please disable Space Age.
stack traceback:
[C]: in function 'error'
pypostprocessing/data.lua:16: in main chunk

I tried to play along by disabling the base mod, but that doesn't seem to be the correct answer.

The main game version is 2.0.72 build 84292.

Any idea what I am doing wrong?

OK I'm stupid. There is a mod named "Space Age" and that is what I was supposed to disable. Clicking the 'disable listed mods' didnt do what I thought it does. It disables the mod that errored, not the mod that is being complained about.