They have a new feature called "API balance" where you can look at the balances in all your exchanges in which you have enabled API integration. I think that should be sufficient for the scenario you are mentioning.
Also Cointracking already takes care of the deposit purchase issue. Since Cointracking will have the details of all the wallets in your exchange it can identify if you are making a trade or if you are moving funds to your wallets from external addresses.
The new transfer function makes it very handy if at least one of the exchanges sends IN/OUT information via API.
It duplicates the transfer and changes buy and sell amount. Some manual actions are totally okay for me :)