It is not as much Windows XP and whatever flavour of visual basic runtimes the skinning tools want, though I guess that could be annoying in 2015, but the new loaders not using a DS skin and all the older programs seem to error out with that setup. It is all still the same underlying theory, save for the DS stuff not being there, but the legacy tools will not work. Equally the various mods, fixes and python skinning tools from modulo, Kuwanger and co were more version specific hacks; prior to the last 2013 run it had been years since the last loader update (late 2006 for the previous official and mid 2007 for the modulo hacked loaders --
http://ezflash.sosuke.com/viewtopic.php?f=12&t=793 , the EZ4 itself kept being updated until April 2009) so that made sense really.
I forget which way around it went for the DS loader and GBA loader section. I believe it used the GBFS (gameboy file system, a popular homebrew file system for the GBA
http://pineight.com/gba/#gbfs ) format to store things, equally it wanted the pictures in a custom/hardware close format for the GBA side of things so they needed to be converted to 16 bit BMP (easier said than done with a lot of image editing programs as it is not a very common format). Most things I have done with it have been more for extracting skins from old loaders than manually building new ones so I will have to read up before I go too much further. As it is BMP for the GBA side of things and thus should be the same size regardless of the input image then you should be able to copy things around/over older parts, on the other hand I vaguely recall some compression from the EZ3 skin days (the EZ4 GBA loader was very much based upon the EZ3 loader, hence the clock for the RTC it does not have).