It's quite easy to change the offsets, using WinTex... and more complicated with XWE.
It's what I done with some sprites of my collections ("Wads1or2.wad", "Wads1to2.wad, AddonFor1.wad" and "AddonFor2.wad"). Playing with my addons let you have sprites correctly looking.
By the way, did you know that the SKY1 is bugged within the Iwad? Don't tell me that my version is screwed, because it's coming from the CD that I bought: "Ultimate Doom : Thy Flesh". This sky has a y offset wrongly declared to be "-8"...
This Doom iwad is dated, on the CD, wednesday june 12, 1996, 16:59:02
A lot of errors like this one are present within the iwads...
So yes, WE have to do the job by ourself.
You could do the same thing?