This started not as a real and proper answer, but to demonstrate that at least on 2.76b, with Sapling 0.2.6, sapling addon worked as you would expect:
So, I suggested you to detail exact blender and sapling versions you are trying. It could also be a bug or a changed behavior...
Meanwhile, I found a 2.79rc2 lying on my disk, so tried also launching Blender-softwaregl (opengl sw emulation due to my crappy notebook), here the addon is named "Sapling Tree Gen", version 0.3.3, it behave like you said: the tree is always at grid origin, no matter where the 3d cursor is.
It seems that there was a big change from 0.2.6 to 0.3.2 labeled as a "major rewrite", I guess starting just before 2.78 release, see this diffusion page.
But, good news! Browsing the sources on that page, I found a single line that reverts the behavior of sapling 0.3.3 to how it was in 0.2.6
find the file
<blender install folder>/2.79/scripts/addons/add_curve_sapling/utils.py
go to line 1604, it should be like
change it to
save the file
- (if it was open, close and) start Blender
- now sapling should behave as it did in 2.76 :)
Note: I've later found a comment by the addon developer stating that he did
"Fix Armature, Tree location generation to 0,0,0 (this was causing fails with armature weights & probably pruning)"
So, use this with caution, and revert if necessary...