It is small indeed.

    $ diff -u <(xxd -g1 shattered-1.pdf) <(xxd -g1 shattered-2.pdf)
    --- /dev/fd/63	2017-02-24 12:25:17.311939732 +0530
    +++ /dev/fd/62	2017-02-24 12:25:17.311939732 +0530
    @@ -10,14 +10,14 @@
     0000090: 72 65 61 6d 0a ff d8 ff fe 00 24 53 48 41 2d 31  ream......$SHA-1
     00000a0: 20 69 73 20 64 65 61 64 21 21 21 21 21 85 2f ec   is dead!!!!!./.
     00000b0: 09 23 39 75 9c 39 b1 a1 c6 3c 4c 97 e1 ff fe 01  .#9u.9...<L.....
    -00000c0: 73 46 dc 91 66 b6 7e 11 8f 02 9a b6 21 b2 56 0f  sF..f.~.....!.V.
    -00000d0: f9 ca 67 cc a8 c7 f8 5b a8 4c 79 03 0c 2b 3d e2  ..g....[.Ly..+=.
    -00000e0: 18 f8 6d b3 a9 09 01 d5 df 45 c1 4f 26 fe df b3  ..m......E.O&...
    -00000f0: dc 38 e9 6a c2 2f e7 bd 72 8f 0e 45 bc e0 46 d2  .8.j./..r..E..F.
    -0000100: 3c 57 0f eb 14 13 98 bb 55 2e f5 a0 a8 2b e3 31  <W......U....+.1
    -0000110: fe a4 80 37 b8 b5 d7 1f 0e 33 2e df 93 ac 35 00  ...7.....3....5.
    -0000120: eb 4d dc 0d ec c1 a8 64 79 0c 78 2c 76 21 56 60  .M.....dy.x,v!V`
    -0000130: dd 30 97 91 d0 6b d0 af 3f 98 cd a4 bc 46 29 b1  .0...k..?....F).
    +00000c0: 7f 46 dc 93 a6 b6 7e 01 3b 02 9a aa 1d b2 56 0b  .F....~.;.....V.
    +00000d0: 45 ca 67 d6 88 c7 f8 4b 8c 4c 79 1f e0 2b 3d f6  E.g....K.Ly..+=.
    +00000e0: 14 f8 6d b1 69 09 01 c5 6b 45 c1 53 0a fe df b7  ..m.i...kE.S....
    +00000f0: 60 38 e9 72 72 2f e7 ad 72 8f 0e 49 04 e0 46 c2  `8.rr/..r..I..F.
    +0000100: 30 57 0f e9 d4 13 98 ab e1 2e f5 bc 94 2b e3 35  0W...........+.5
    +0000110: 42 a4 80 2d 98 b5 d7 0f 2a 33 2e c3 7f ac 35 14  B..-....*3....5.
    +0000120: e7 4d dc 0f 2c c1 a8 74 cd 0c 78 30 5a 21 56 64  .M..,..t..x0Z!Vd
    +0000130: 61 30 97 89 60 6b d0 bf 3f 98 cd a8 04 46 29 a1  a0..`k..?....F).
     0000140: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
     0000150: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................
     0000160: 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00 00  ................

The differences are confined to two SHA-1 input blocks of 64 bytes each. The first block introduces a carefully-crafted set of bit differences in the intermediate hash value (IHV), which are then eliminated in the second block. After the IHVs synchronize, all future blocks can be identical because SHA-1 can be trivially length-extended.