Is there a way to specify the compiler and/or linker options int eh preferences file, or some other easily modified file?
It's all covered in the "readme.txt" file in the same place as you obtained the IDE.
If you are looking to save memory space these optimizations go a lot further to conserve ram than the standard IDE:
-g -Os -Wall -ffunction-sections -fdata-sections -funsigned-char -mcall-prologues -Wl,--relax,--gc-sections -funsigned-bitfields -fpack-struct -fno-inline-small-functions -fno-split-wide-types
Good linker options: