Amazingly helpful responses, thanks.
[MENTION=424205]Salamandrine[/MENTION] - no it has two chainwheels up front, 10 speeds total.
What I've tried so far is check the limit screws and do test drives with different settings - and I also managed to change the angle and distance of the chain (between large cog and pulley) just a little bit by moving the axle back in the dropouts some 1 cm / 0.4 inches - there was still some room for that, as the axle was currently set very close to the forward-most position.
It made no difference, not even slight.
The issue could be either the freewheel or the chain, even though neither appeared worn to the naked eye - I haven't measured the chain just yet. Over the course of these 2 years I have ridden - very very rough estimate - about 400+ km / 250+ miles on the bike, but 90% of that has been light city cruising and I would say I'm way more gentle to the drivetrain/chain than a lot of pedalers while shifting etc, just a gut feeling of course but I always like to treat this bike with extra care and avoid rough pedaling etc.
I'll see if I can think of more ways to reduce the gap between the large cog and pulley a little. Grinding the stop on the claw bracket as suggested by [MENTION=185430]dddd[/MENTION] is an option, although I think I got the distance changed about that amount when pulling the axle back a bit - and nothing changed.
I think it doesn't have to do with the chain hitting anything sideways (cage) because the uneven feel is more 'heavy and thumpy' (instead of 'clanking and rattly') with almost no sound, just more of a feeling while pedaling.
Easiest next step would probably be to change the chain, I also know a bike shop in my city who has a replacement Maillard Atom 66 freewheel if needed. I think I've sometimes noticed that the freewheel can move the drivetrain/pedals a little bit (momentarily) when just walking with the bike next to me, I don't know if that indicates the freewheel might need replacing at some point anyway.