OK. There's a bit of confusion here with levels/ids that may be hard to resolve. In Amira the Id field stores an arbitrary integer identifier that has nothing to do with the pixel value. read.amiramesh.header stores this in the id column of the Materials data.frame in the header information. Meanwhile level corresponds to the 0-indexed pixel value. However the nat::materials then returns a data.frame with a column id that is the pixel value+1. I think the conclusion is that for general use we can assume that result of materials contains an id column that is pixel+1 and Amira's internal id is not very relevant for anything.

h=read.amiramesh.header("~/projects/VFB/JFRCtempate2010.mask130819.am")
> head(h$Materials, n = 21)
         id     col level
Exterior  1   black     0
AME_R     2 #3C29CC     1
LO_R      3 #29CC99     2
NO        4 #47CC29     3
BU_R      5 #2960CC     4
PB        6 #CC8229     5
LH_R      7 #CC2855     6
LAL_R     8 #CC6C28     7
SAD       9 #9CCC27     8
CAN_R    10 #EBBD79     9
AMMC_R   11 #47CC29    10
ICL_R    12 #CCA229    11
VES_R    13 #FF7E7E    12
IB_R     14 #B529CC    13
ATL_R    15 #7E7EFF    14
CRE_R    16 #79EB93    15
MB_PED_R 17 #CC69C0    16
MB_VL_R  18 #29CCB4    17
MB_ML_R  19 #A529CC    18
FLA_R    20 #282DCC    19
LOP_R    22 #7E7EFF    20

> head(materials("~/projects/VFB/JFRCtempate2010.mask130819.am"), 21)
       name id
1  Exterior  1
2     AME_R  2
3      LO_R  3
4        NO  4
5      BU_R  5
6        PB  6
7      LH_R  7
8     LAL_R  8
9       SAD  9
10    CAN_R 10
11   AMMC_R 11
12    ICL_R 12
13    VES_R 13
14     IB_R 14
15    ATL_R 15
16    CRE_R 16
17 MB_PED_R 17
18  MB_VL_R 18
19  MB_ML_R 19
20    FLA_R 20
21    LOP_R 21

material should keep col and levels field #284

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