Hi rebaj83,
I think it depends on the size of your input image.
Yes... if you use a small vertical FoV in your Cylindrical pano as input image, the resulting "false Equirectangular" image (adding Blank top and bottom) can be near similar to the same input image converted to "real" Equirectangular... But not equal... If an exact correct projection is not a matter then it's ok. But if you want a correct projection from Cylindrical to cube, using Ktransform to do so, you must convert your Cylindrical pano to Equirectangular.
I suggest you to compare from your Cylindrical pano with Blank top and bottom added and the same Cylindrical pano converted to Equirectangular. You will notice the difference...
Perhaps Klaus can improve his Ktransform tool to make possible a direct convertion from Cylindrical to cube...
Salut.