A creature that contracts lycanthropy apparently does so instantaneously upon suffering a natural lycanthrope's bite and failing the Fortitude saving throw. The supernatural ability curse of lycanthropy says
Any humanoid or giant hit by a natural lycanthrope’s bite attack in animal or hybrid form must succeed on a DC 15 Fortitude save or contract lycanthropy. If the victim’s size is not within one size category of the lycanthrope (for example, a hill giant bitten by a wererat), the victim cannot contract lycanthropy from that lycanthrope. Afflicted lycanthropes cannot pass on the curse of lycanthropy. (MM 176)
In the example above, oddly, a wererat in hybrid form is Medium and a hill giant Large; those are within one size category. So assuming Skip Williams means the wererat is in animal form, this means the curse of lycanthropy checks the potentially afflicted creature's size category only when the creature initially contracts the curse.1
That's your in.
So, although the DM may (and should) care, the curse of lycanthropy apparently doesn't care how the victim achieved the size category he had when the victim became an afflicted lycanthrope, nor does the victim's size category seem to matter after the victim's afflicted. He's an afflicted lycanthrope now with whatever form of lycanthropy he was afflicted with then, regardless of his actual, for-reals size category.
Seriously, talk this over first with the DM.
This means that, for example, if the DM determines the goliath racial trait powerful build counts toward the size categories of lycanthropic afflictions a goliath is subject to, were such a goliath also to be the subject of an effect like enlarge person, such a goliath would count as a Huge creature for lycanthropic affliction purposes. Then, if, while so virtually Huge, that goliath were bitten by a were-roc storm giant that was in hybrid form, and the goliath failed the Fortitude saving throw (DC 15), that goliath could become an afflicted were-roc. All assuming the DM is on board, of course.
Given the likelihood of a high Constitution score and the inability to voluntarily fail saving throws against anything but drugs, psionic powers, and spells, the affliction may need a few bites to take. A method of healing between bites might be wise.
It will be challenging for such a lycanthrope to breed with similar lycanthropes to produce natural lycanthropic offspring. I mean, if that's a concern.
Note that if a DM ever pits my PC against a gnome who we later learn had once inadvertently used a scroll of the 7th-level spell giant size [trans] (CM 109-10) to become Huge only to be bitten immediately afterward and contract lycanthropy so that we PCs now have to fight a Gargantuan 36-Hit Die were-giant squid gnome, I am deleting this answer. Don't think I won't.
1 The counter to all this is, of course, that Williams means the animal part of being a lycanthrope, and the typical dire rat is Small. This puts a kibosh on the whole thing. But because we want this to work, we won't go there.