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As stated in some other threads, the image from the BSP is meant to be built as a 32 bit system. So going with 64 bits using the BSP would probably require a lot of work.
Regarding the 64 bit flag, I believe this is not provided by the target machine but by the host computer. In this case it would be your computer with Ubuntu 14.04.
We haven’t try to build an image using a 64 bit kernel so there’s not much information we can provide, but I’m wondering if you have checked this link before: https://edison.internet-share.com/wiki/Using_a_vanilla_Linux_kernel_with_Intel_Edison. This user has been trying to replicate the steps from a Russian website where someone was able to boot Edison using vanilla kernel without any patches. So I suggest you to check that information, his progress can also be seen here: https://communities.intel.com/thread/75472.
@Pablo, the author of that Russian article is Andy Shevchenko who is a kernel developer and posting his edison work here https://github.com/andy-shev/linux/tree/eds. Thanks to Andy a lot of edison specific stuff has already made it into the latest kernel and probably more to come. Looking at the e-mail address in his commits <email@example.com> he may be a colleague of you :-)