Mark does some extra annotation where he re-aligns the probes. These data are in the 'ExtraInfo' table:

> con <- illuminaHumanv4_dbconn()
> dbGetQuery(con, "select * from ExtraInfo limit 10;")
     IlluminaID ArrayAddress               NuID ProbeQuality CodingZone
1  ILMN_3166687      5270161 fVO7UPeDN.UnC595UU     No match       <NA>
2  ILMN_3165565      4230037 iEi8IfI0mJK7GVaF_o     No match       <NA>
3  ILMN_3164808        60372 xhGZ_EYeDUnwiV5BmM     No match       <NA>
4  ILMN_3165363      5260356 ieQ5TwQXyRrP1LJ64k     No match       <NA>
5  ILMN_3166504      6060692 cnbRQdtGY2AyfocO1o     No match       <NA>
6  ILMN_3164750      6370471 9PgL_oqHPRLMjivvko     No match       <NA>
7  ILMN_3166430      1710435 HUSTVLbg8LMCQdRQ70     No match       <NA>
8  ILMN_3165745      1400612 ZdnuDceSBzq.nJmWs0     No match       <NA>
9  ILMN_3164915      5130189 rqBYPEQbChsXnXFVgU     No match       <NA>
10 ILMN_3165415        70278 rVszqdr4Xc_pvvhWD0     No match       <NA>
                                        ProbeSequence SecondMatches
1  CCCATGTGTCCAATTCTGAATATCTTTCCAGCTAAGTGCTTCTGCCCACC          <NA>
2  ACAGAGTTAAGACTTAGATCAGCGAGCAGGTGTACGCCCCGGACCTTGGG          <NA>
3  GACACGCGCTTGACACGACTGAATCCAGCTTAAGAGCCCTGCAACGCGAT          <NA>
4  CTGCAATGCCATTAACAACCTTAGCACGGTATTTCCAGTAGCTGGTGAGC          <NA>
5  GCTCGTCACCAACTCGTCACGCGATCGAAATAGCTTGGACTAATGTCCGG          <NA>
6  ATTGAAAGTTTGGGAGGGACTATTCACAGTATAGATGAGGTTGTTGCAGG          <NA>
7  CCACAGCATCCCAGTCGTGAATTAAGTATAAAGCAACTCCACCAATGTTC          <NA>
8  CTCGCTGTGAATCTACTGCAGAACTATGGGTTTGCTAGCGCGCCGGTATC          <NA>
9  GGGAACCGAATTACACAACGTAAGGACGTACCTGCTCCTACCCCCGAACC          <NA>
10 CCCGTATATGGGCTCGGTTGACCTCTATTGGGCGTTGTTGACCCGAATTC          <NA>
   OtherGenomicMatches RepeatMask OverlappingSNP EntrezReannotated
1                 <NA>       <NA>           <NA>              <NA>
2                 <NA>       <NA>           <NA>              <NA>
3                 <NA>       <NA>           <NA>              <NA>
4                 <NA>       <NA>           <NA>              <NA>
5                 <NA>       <NA>           <NA>              <NA>
6                 <NA>       <NA>           <NA>              <NA>
7                 <NA>       <NA>           <NA>              <NA>
8                 <NA>       <NA>           <NA>              <NA>
9                 <NA>       <NA>           <NA>              <NA>
10                <NA>       <NA>           <NA>              <NA>
   GenomicLocation SymbolReannotated ReporterGroupName ReporterGroupID
1             <NA>              <NA>        ERCC-00162      ERCC-00162
2             <NA>              <NA>        ERCC-00071      ERCC-00071
3             <NA>              <NA>        ERCC-00009      ERCC-00009
4             <NA>              <NA>        ERCC-00053      ERCC-00053
5             <NA>              <NA>        ERCC-00144      ERCC-00144
6             <NA>              <NA>        ERCC-00003      ERCC-00003
7             <NA>              <NA>        ERCC-00138      ERCC-00138
8             <NA>              <NA>        ERCC-00084      ERCC-00084
9             <NA>              <NA>        ERCC-00017      ERCC-00017
10            <NA>              <NA>        ERCC-00057      ERCC-00057
   EnsemblReannotated
1                <NA>
2                <NA>
3                <NA>
4                <NA>
5                <NA>
6                <NA>
7                <NA>
8                <NA>
9                <NA>
10               <NA>

So I think he does something much more sophisticated than using the Illumina mappings straight away. However, for this and all other ChipDb packages, there is only one mapping, in the end, that matters, and that is from Illumina ID -> Entrez Gene ID. The ChipDb packages may contain other tables, but when you use them to do a given mapping, the AnnotationDbi package will attach the 'probes' table of the ChipDb package to the required table in the respective OrgDb package (org.Hs.eg.db in this case) and then do a SQL query using the two tables.

So for instance if you want the Ensembl Trans ID for an Illumina probe, you will end up attaching the 'ensembl_trans' table from org.Hs.eg.db and then doing an inner join between the probes table in the illuminaHumanv4.db package and the ensembl_trans table from org.Hs.eg.db, using the Entrez Gene ID (the table index) to do the join. So we are dependent on what NCBI (and probably Ensembl) think are the correct mappings between Entrez Gene and Ensembl trans, as we just use what we can get from NCBI to set up the org.Hs.eg.db package.