I really can't tell what your trying to accomplish.
X: is the booted .wim image containing the PE operating system
Y: the ROOT directory of whatever media your building it contains the boot.wim file that is mounted as X: and also programs separate from the .wim image (if your running from a CD/DVD/USB they are on the root of the disc. if your running from CD/DVD Y: is not writable)
there are several reasons why you might want to have the programs located in X: mostly if you are running from CD/DVD their directory will be writable (in case they need to read/write to a config file or download something) or if you are booting the image directly over PXE which only knows whats in the .wim...it can't see anything else.
reasons for running from Y: is that since they are not packed in the .wim image you can update them independent of rebuilding the project. it also makes building slightly faster as they don't have to be compressed into the .wim
lots of app scripts give you a checkbox or scrollbox to choose if you want to run from RAM (pack in .wim) or from CD (Y:)
if you want a different behavior then that you will need to rewrite the project to pack whatever programs you want into a separate .wim and mount it to a letter of your choosing