The latter. 64-bit compilation is available only through a set of patches.
You'll find instructions for building an x64 SDK here:
http://wiki.panotools.org/Hugin_SDK_(MSVC_2008)
SDK patches are here:
http://sourceforge.net/tracker/?func=detail&aid=2789320&group_id=77506&atid=
550443
Hugin patches are here:
http://sourceforge.net/tracker/?func=detail&aid=2787607&group_id=77506&atid=
550443
Enblend/Enfuse patches are here:
http://sourceforge.net/tracker/?func=detail&aid=2787615&group_id=123407&atid
=696411
Once you have a 64-bit SDK, it's just a simple task of using CMake for Hugin
as the same process as 32-bit. If you followed the wiki page, the 64-bit
libs will have the same filenames as the 32-bit libs, so you won't just be
able to switch configurations to compile 32-bit and 64-bit Hugin (instead,
you'll need separate SDKs).
By all means, please do. There's definitely a need for someone to provide 64-bit builds. I've refrained from it myself, though I provided the 64-bit steps, because I'm only able to offer a patent-free installer. As I haven't had a chance to test through different scenarios with a mixed 32-bit CP generator (such as those obtained from the 32-bit installer) with a 64-bit tool-chain, which I suspect may have some WoW64 issues, I haven't bothered to post a patent-free installer.
The only other thing I'd add to that, if you're looking to build the installer, is that the ISS files may offer a little bit of trouble for you. Specifically, the hugin.iss file expects panomatic, matchpoint, and matchnsift to be around. Match-n-sift has perl dependencies, and there exists no "perl to exe" type compilers for 64-bit AFAIK, which is how the 32-bit is/was distributed. Panomatic is available at http://aorlinsk2.free.fr/panomatic/?p=home , although I haven't seen any SDK notes for compiling it (I don't use it myself). As for matchpoint/autopano-sift-C, following the SDK steps you should end up with those binaries. There are also two typos in the ISS - PTBatcher and PTBatcherGUI should both end in .exe (naturally)
The installer generated will be a 32-bit installer, so registry keys/file system paths will reflect the WoW64 counterparts, unless you make changes to the .iss file(s). This can be tweaked by introducing the name/value pair ArchitecturesInstallIn64BitMode=x64 in the [Setup] section, but I haven't had a chance to spin it through my test VMs, so I'm not sure what effect (if any) this might have to the actual install process.
The support for 64-bit Windows with Hugin is one of "with caveats" - It was something fairly late in the game that has not yet had extensive testing, and is only available via supplementary patches that will eventually make their way into trunk. Myself, I've been running it without difficulty since I posted the patches in May, using a 32-bit installer, and full 64-bit binaries for everything else, installed via the .iss file (with various CP generators disabled), so it should be 'ready'... but that's just one test machine / one tester.
Also, what's the "CP generator" (control point generator executable?), and what's with the patent situation?