Unfortunately this is not true as Adobe only supports Flash for Windows, Linux and Mac on x86/x86_64 processors. Though as far as Desktop OSes are concerned, non x86/x86_64 processors have such a small user base that it is not really feasible for a commercial closed source project to develop for. But this, by its very definition makes it non portable. Adobe has even recently abandoned Flash for Mobile, so all Smart Phones, Tablets, and like devices will be forever without flash, again not too portable when you consider that these devices are consuming a huge percentage of the average users web browsing.
But we are not talking about supporting on just a computer OS (if we were, your portabilty argument, while not entirely valid, would be sufficient) , but as FFXIV is slated for the PS3, and at some point (possibly) the 360, we need to consider other platforms. And with this broader view, Adobe Flash is a very unportable solution.
From my own experience, and that of many millions of others, Flash is horribly unstable. Steve Jobs (I am not a fan of Apple by any means, in fact quite the opposite) even called it "closed" (as in closed source, not portable), "unstable" and "bug prone". Flash is a nightmare (for end users) plain and simple.
They actually happen to be redoing the entire client (see 2.0) and have stated that its likely to use Flash for user add ons. So this isnt just a unfounded fear that they might choose Flash, they have made it plain that its being considered.
At the end of the day, if there is a problem with code, I want SE to be able to dig in and fix it. I do not want to have to wait for Adobe to issue a fix, and I do not want add ons to be a PC only feature when an in house solution would be usable by everyone. I do understand, however, that SE is doing a hell of a lot of work getting the 2.0 engine ready, and them using a pre made solution for add ons would mean they didnt have to give much resources to this, but its a sacrifice that has too many drawbacks.