Well it is pretty clear to me. When you use AMD64 port of FreeBSD the OS has access to both 32bit parts of the processor and in addition to 64bit parts of the processor. Having a 64bit processor basicly means the OS has access to more resources. The programs might take advantage or not is another question of course. However compilers do optimizations. Agreed, some programs might use slightly more memory but nowadays even laptops ship with 2gb of memory, having a process which use 300mb memory use 400mb instead is negligible downside.
Here is some test results of various applications (not on FreeBSD but...)
http://www.scribd.com/doc/363677/Ben...it-mode-Ubuntu
According to these results most applications give 20-30% speed increase and some even 100% and only one of them is mentioned to be using noticeably more amount of memory.
So, if one considers pros and cons of this, if you have a 64bit processor you would be better of using 64bit capable binaries, not only for better speed, but also for being able to utilize full capabilities of the processor. Otherwise paying for 64bit processor but use it as 32bit doesnt make much sense.