Yes, they don’t want you editing in place core parts because as noted you can break things (and your changes will get overwritten at the next parts update from github as well which may not have been happening when that readme was written). In general pick a part with something close to what you want (a 5050 led I think) right click on the part and select edit part with parts editor. Then file-save part (which will put the new part in the mine parts bin), right click the part in mine and select export part. That will save the part as an fzpz file. Use an unzip program (I use 7zip) to unzip the fzpz file and you will have the fpz file and the 4 svg files that make up the part. Modify the svg file you want then use 7 zip again to zip all 5 files to the same or a new file name and up load it to fritzing to test. Note if you may mistakes it is possible to hang Fritzting and need to delete the user files so make sure you have a backup of the directory or your sketches before doing this. What may be easiest for you is to copy the appropriate svg from (in Windows)
C:\fritzing\fritzing.0.9.3b.64.pc\fritzing-parts\svg\core\pcb
to another location edit the svg there (so as to not change the core copy) then load it with the parts editor in to the part that you want.
If you haven’t read them these two tutorials on parts making may help you (most of the above are in one or the other):
Peter