It's not that index doesn't use Boyer Moore, it's more that the regex engine doesn't always use Boyer Moore. If the regex engine comes to the conclusion to use screaminstr, it will use that instead of Boyer Moore.

I guess that if you change your data to be more favorable to Boyer Moore, the results will reverse as the regular expression will still not use Boyer Moore.

Update: Even weirder. Looking at the log of use re 'Debug','ALL';, it claims that fbm_instr() is used:

C:\Projekte>perl -Mre=Debug,ALL -e "shift=~/abcdefghijklmnopqrstuvwxyz
+X/" abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabcdef
ghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzXabcdefghijklmnopqrstuvw
+xyzabcdefghijklmnopqrstuvwxyz
Compiling REx "abcdefghijklmnopqrstuvwxyzX"
Starting first pass (sizing)
 >abcdefghij... |   1|  reg
                |    |    brnc
                |    |      piec
                |    |        atom
Required size 9 nodes
Starting second pass (creation)
 >abcdefghij... |   1|  reg
                |    |    brnc
                |    |      piec
                |    |        atom
 ><             |  10|    tail~ EXACT <abcdefghijklmnopqrstuvwxyzX> (1
+) -> END
first:>  1: EXACT <abcdefghijklmnopqrstuvwxyzX> (9)
first at 1
Peep:Pos:0/0 Flags: 0x0 Whilem_c: 0 Lcp: 0 Last:'' 0:0/0 *Fixed:'' @ 0
+ Float: '' @ 0/0
Peep>  1: EXACT <abcdefghijklmnopqrstuvwxyzX> (9)
  join>  1: EXACT <abcdefghijklmnopqrstuvwxyzX> (9)
pre-fin:Pos:27/0 Flags: 0x0 Whilem_c: 0 Lcp: 0 Last:'abcdefghijklmnopq
+rstuvwxyzX' 27:0/0 *Fixed:'' @ 0 Float: '' @ 0/0
post-fin:Pos:27/0 Flags: 0x0 Whilem_c: 0 Lcp: 0 Last:'abcdefghijklmnop
+qrstuvwxyzX' 27:0/0 *Fixed:'' @ 0 Float: '' @ 0/0
commit: Pos:27/0 Flags: 0x0 Whilem_c: 0 Lcp: 0 Last:'abcdefghijklmnopq
+rstuvwxyzX' -1:0/0 *Fixed:'abcdefghijklmnopqrstuvwxyzX' @ 0 Fl
oat: '' @ 0/0
minlen: 27 r->minlen:0
Final program:
   1: EXACT <abcdefghijklmnopqrstuvwxyzX> (9)
   9: END (0)
anchored "abcdefghijklmnopqrstuvwxyzX" at 0 (checking anchored isall) 
+minlen 27
r->extflags: CHECK_ALL USE_INTUIT_NOML USE_INTUIT_ML
Guessing start of match in sv for REx "abcdefghijklmnopqrstuvwxyzX" ag
+ainst "abcdefghijklmnopqrstuvwxyzabcdefghijklmnopqrstuvwxyzabc
defgh"...
Check offset min: 0 Start shift: 0 End shift 0 Real End Shift: 0
fbm_instr len=157 str=<abcdefghijklmnopqrst>
Found anchored substr "abcdefghijklmnopqrstuvwxyzX" at offset 78...
Check offset min:0 max:0 S:78 t:78 D:0 end:157
Starting position does not contradict /^/m...
Guessed: match at offset 78
Freeing REx: "abcdefghijklmnopqrstuvwxyzX"
[download]

So, I don't understand what happens, or how the RE engine is faster than index when they both fire up fbm_instr.