Whole portfolio allows you to optimize the location of each asset for tax advantages and lowest cost (expense ratio). For example, assets that pay a higher proportion of dividends would be held preferentially in a tax advantaged account (IRA, 401k etc) over a taxable account.
As another example, my TSP account (basically a 401k for federal government employees) has low expense ratios across the board, but the savings is greatest in its international fund over similar offering by vanguard. Therefore all of my international holdings are in my TSP account, and my vanguard accounts are all US stock market.
It can be harder to keep track of your total asset allocation across accounts this way, but that is easily solved by account aggregation tools like personal capital, and mint.
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