But by using leverage with a 'small' position I'm still borrowing the high interest rate while earning the low rate on the left over money. I'm trying to avoid that. Trading using subaccounts is limited since you cant buy NZD and others
Huh? You seem to be confusing "account leverage" and "trade leverage." The latter obviously can't exceed the former, but can be a small fraction of it. 10:1 - 50:1 simply sets an upper bound for maximum (initial) "account leverage," across all open trades combined. A given trade might have "trade leverage" of 10:1, 1:1, 0.2:1, 0.005:1, etc., all the way down to 1 unit trade size. No one is forcing you to use any leverage on a given trade, unless you want to. What "borrowing" are you talking about? Also, limited trading in sub-accounts... are you sure about that? Of course, you can trade NZD/USD or AUD/NZD in a sub-account. Anything you can do in the primary account, trading-wise, you can do in a sub-account.
I meant creating a sub account in NZD SGD, etc, that is not possible. If you 'trade' through moving money between subaccounts(one day you 'sell' your USD and send to a subaccount in EUR) your in good shape because your give up the lower interest rate on the USD subaccount and get the low rate in the EUR subaccount(initiating a synthetic negative carry trade). But if you have a USD subaccount and initiate the same trade through buying EUR/USD since you will be using margin you will be charged the HIGH rate on the dollar side and get paid the low rate on the EUR side, the carry is a little worse that way. Maybe I'm wrong but so far this looks to be true
You can't create a sub-account in NZD, SGD, etc., because you can't create a primary account in NZD, SGD, etc. Those are not valid account (primary or sub-) base currencies, which are: AUD, CAD, CHF, EUR, GBP, JPY, USD. Once again, I am not aware of any difference, trading-wize, between your primary account and sub-accounts. As to trading by transferring funds among sub-accounts denominated in different currencies, yes, your scenario 2 is "a little worse" indeed. According to this, by around $2.02 per lot per day. Which is 0.0015% a day, or 0.55% a year. Go for it.
I'm not sure how you used that calculator but I believe you lose the spread between lend and borrowing interest per year. so for the usd thats roughly +0.5% in carrying cost a year on your open USD short positions(if you do through subaccounts your 0.5% better off). Maybe I'm wrong. I hope I'm wrong