BH currently holds ~27% (about $29B) of Heinz-Kraft, and don't forget the 100% buyout of BN-SF (in 2010 was worth around $44B).
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Berkshire owns its shares in Kraft Heinz as part of a control group (with 3G) and thus accounts for those holdings a different way. It uses the equity method rather than the fair value method. That means, among other things, that it reports earnings each year (and quarter) based on the net earnings of Kraft Heinz. If Kraft Heinz makes $1 billion, Berkshire reports a percentage of that amount (equal to its percentage ownership of Kraft Heinz) as its own earnings and then adjusts the value of its Kraft Heinz ownership accordingly on its balance sheet. That balance sheet value does not equal the fair market value of those Kraft Heinz shares (i.e. the current trading price per share times the number of shares Berkshire owns) - it is considerably less.
With the other stock holdings we're talking about, Berkshire accounts for them using the fair value method. They are valued as assets based on their market value - i.e., based on current stock prices. Increases in their value aren't counted as earnings for Berkshire until they are sold. (They are counted as unrealized gains within Berkshire's statement of its comprehensive income, but that's something different.)
So, in a sense Berkshire does own more Kraft Heinz than it does Coca-Cola or Apple, but that ownership is accounted for quite differently. Because of the accounting method it uses for its Kraft Heinz ownership (which is the result of it being considered to have significant influence over the operations of Kraft Heinz), Berkshire wouldn't typically list Kraft Heinz as one of its top equity holdings. The relationship between itself and that investment is seen as of a substantially different nature.
The situation with Burlington Northern Sante Fe is also different, even more so. It's among Berkshire's operating businesses. Berkshire is a holding company that has lots of businesses, and businesses of many kinds - e.g., insurance, manufacturing, railroad. They all contribute to Berkshire's operating results. In (perhaps overly) simplistic terms, they are part of what Berkshire does rather than things that Berkshire invests in. Berkshire has, of course, invested in those operating businesses; but it's done so in ways that make them part of Berkshire itself rather than just being stock holdings. Looking at those operating businesses respectively, we may be able to estimate a value for them or estimate how much of Berkshire's value each one fairly represents. But they don't really have clear market values as Berkshire's equity holdings do. And they wouldn't be considered investment holdings in the sense that the likes of Apple and Coca-Cola and American Express would. Berkshire owns Geico, e.g., but Geico wouldn't be considered a holding in the way those others would. It's more fundamentally a part of what Berkshire is and does.
