I have the same issue as the OP with the complication of having variants for each product which determine the final price. This makes the workaround above unusable.
All I seem able to do is require payment in full or ask customers to email if they would rather make a deposit. This is far from ideal.
Has a workaround I can use or a proper feature been added yet to address this? Maybe it's technically hard, but I'm surprised it is lacking.
No reply. So I'm infer this is a feature that won't be added. It is important for my business, so next year I'll move on from Squarespace. What a shame.