DoCoMo is heavily into mobile payments, and is under the delusion that it can keep things that way. THAT is what this is all about.
I imagine that they could do what they do with an App Store app (though I don't know how their system works) but they'd presumably have to give Apple a cut of that on-going revenue, and that's what they're trying to avoid.
The issue is less, I would say, about pre-loaded apps and more about the split of mobile payments revenue.
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Don't get caught up in the hype.
Japan has been very big in the past on technology that superficially looked cool but was actually a ridiculously stupid and impractical idea.
Their analog (rather than digital) HDTV system was one example; broadcasting movies over the cell network is another example --- solving a non-existent problem in a way that will never be practical because the bandwidth IS NOT THERE.
There's a reason no-one speaks in awed tones about the dominance of Japan in the mobile market. A solution that takes off has to actually WORK (which means things like be able to scale to the realities of the practical world) rather than just be a neat tech demo.