This is a great point, and thinking about it I can't definitively answer it either: If we change the puppet prioritization to default, the general -25% on yields would be much more balanced, but there's no saying what the puppet will build - and it could just become a money or happiness pit without much reward given the puppet's terrain - if there's a lot of production but low food/population, say, or a lot of food but little production - but these are probably outlier examples. The plus-side of making this change is that the puppet will build more science and culture buildings, therefore benefiting the empire in a more balanced way, which I admit would be great.
Otoh, I think the gold focus is really quite brilliant, because it guarantees 1) the puppet's build order will be fairly predictable, 2) the benefit will always be useful, 3) growth will be curtailed (but generally not halted because of the gold on rivers) and 4) any maintenance costs incurred by it's buildings will be mitigated and thus won't be seen as a drain. However, a bit less gold in VEM is desirable, so I think I'd still prefer leaving them on gold focus with a culture, science, and (increased) gold penalty for gameplay reasons, and one could argue that the gold penalty is the general maintenance costs for keeping the puppet - but trying out the other route in a beta would certainly be worthwhile.