If there is a way to shift by pixels (beyond clicking however many bits forward and pressing convert again) I have not seen it on CT2. I would love it as DS games do like to put random amounts of padding in their headers for all files and that makes palette format reverse engineering annoying (I would have stuck with Tiled2002 which has such features but it is not great for custom tile sizes and the DS does love those).
Source code. I have some of the very old source code (2007 where 2010 saw the last versions, and a lot of newer developments missing--- nowadays most of the text is in an external file, here is was still buried in the source code) but I would be impressed if you managed to get it to compile. I mainly only link it to people that are curious and might be able to pull something from it, still for the searchers http://filetrip.net/nds-downloads/utilities/download-crystaltile2-source-code-september-2007-f31478.html
The tileGGD stuff I linked mainly as it is really flexible as far as 2d stuff goes, about the only problems I have really had is with some of the odd DS edit, meant to make sure to say it was the hardware 3d texture formats rather than just normal textures, texture formats but most things are troubled by those. Not having an editor is probably its only downside there.
I am not sure what you mean by the "2-dimensional bpp encoding instead of the standard 1-dimensional used". If you just mean the standard "change the encoding" thenhttp://gbatemp.net/pix/32303/6wizardozndsdemohack15jul2011.png
Where it says GBA 8bpp on the image above if you click that then you have a whole bunch of options, probably the best I have seen in any tile editor (tileggd probably still beats it though). There is a keyboard combo as well but I can not remember it (more or a muscle memory thing and I have not got a windows machine set up with it right now).