I'm not a programmer, I just have lots of Ataris (and a degree in computer science). Anyway, I thought BPEG was lossless. There is some compression in place on the Doom cart, that's for certain - the Loading message at the start of each map, if there was no compression there would be no leadtime because the game could fecth/execute right out of the cart's address space. Could just be Lempel-Ziv or Huffman, I don't know.
They did manage to shoehorn the whole game into 6MB which is impressive. The maps in the Jag version are identical to those in the playstation version (I don't know if iD made a 'standard' set of reduced maps for low storage space systems).
Who even cares as long as it happens? Of all the Dooms I've played the Jag version was the best IMHO (given the playability/hardware ratio)