This is certainly still possible with Commerce 3 and Craft 3.
In a custom plugin or module you can listen for the
Transactions::EVENT_AFTER_CREATE_TRANSACTION event and amend the transaction amount at this point in the process.
For example, you could make your own payment form that includes a
partPaymentAmount field and posts to the normal
commerce/payments/pay controller action.
Then in your event listener to the
Transactions::EVENT_AFTER_CREATE_TRANSACTION event, test to see if a value exists for the
partPaymentAmount POST variable. If it does, amend the transaction amount accordingly. The payment should proceed with the amended amount, so long as it is still a valid amount to pay against the current order (i.e. it is less than or equal to the total amount of the order).
The nice thing about doing it this way is that it is a very light touch on Commerce and still utilises the existing Commerce workflow for processing the transaction and making sure that everything is updated properly.