Hi Lukas,
I think I understand what you'd like to achieve - but I think I would try to do it in a different way.
Instead of having a 'Part 1' and a 'Part 2' as separate parts that are joined to make a 'Part 3' (that you want to be automatically updated by changes to 'Part 1' and 'Part 2), I think I would try to make the overall combined part as my main part, but in such a way that I could suppress some features of it so that it becomes only 'Part 1' or suppress other features so that it becomes only 'Part 2'. In this way 'Part 1' and 'Part 2' would be configurations of the overall part.
Apart from that, I'd most probably try to have my origin of the overall part (and ideally at least the base feature too) be in a place common to both configurations or at a point where they're joined - this way both configurations have their origin in or on the part and not outside it.
I understand this might not help!! - but I hope it does!
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