This is why:
RESOURCES (available also as long-options)
aterm accepts application defaults set in XAPPLOADDIR/aterm (compile-
time defined: usually /usr/lib/X11/app-defaults/aterm) and resources
set in ~/.Xdefaults or ~/.Xresources. Note that when reading X
resources, aterm recognizes two class names: XTerm and Aterm. The
class name XTerm allows resources common to both aterm and xterm to be
easily configured, while the class name Aterm allows resources unique
to aterm, notably colours and key-handling, to be shared between dif-
ferent aterm configurations. If no resources are specified, suitable
defaults will be used.
Read the man aterm for further info.
If you want your aterm to use just aterm resources then you should use -name "name" command line option....
aterm -name terminal
Then you change or add
aterm*saveLines:32767 and so on...
terminal*saveLines:32767 and so on in ~/.Xdefaults
Then aterm should use yous "terminal" resources...