If I have understood correctly what you require, use the "word boundary" asserstion (\b), see perlre.

use strict;
use warnings;

use 5.014;

my $path   = q{XX.YY.ZZ};
my $str    = q{(ABC | (~dEf & hI_J & endxxx)) & ~LMn if ~xYz end};

# Make a compiled regex of an alternation of the terms to exclude.
#
my $rxExcl = do {
   my @excl = qw{ if else 1'b0 end };
   local $" = q{|};
   qr{(?x) (?: @excl ) \b};
   };

my @posns;
push @posns, pos $str
   while $str =~ m{(?x)   # Use extended regex syntax
      (?<! [A-Za-z_] )    # Match at a point not preceded by 
                          #    letters or underscore
      (?=  [A-Za-z_] )    # And which is followed by letters
                          #    or underscore
      (?!  $rxExcl )      # But not followed by any our terms
                          #    to exclude
      }g;

substr $str, $_, 0, qq{$path.} for reverse @posns;
say $str;
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The output.

(XX.YY.ZZ.ABC | (~XX.YY.ZZ.dEf & XX.YY.ZZ.hI_J & XX.YY.ZZ.endxxx)) & ~
+XX.YY.ZZ.LMn if ~XX.YY.ZZ.xYz end
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I hope this is what you want.

Thanks John, that works, you're awesome! By the way, what does this line do? qr{(?:@excl)};

... what does this line do? qr{(?:@excl)};

That statement, which by the way is really
    qr{(?x) (?: @excl ) \b};
interpolates the strings that have been assigned to the  @excl array into a pre-compiled  qr// "regex object" (see Regexp Quote-Like Operators). The interpolation is under the control of the  $" special variable (see perlvar), which has been assigned the  '|' string, which is the regex alternation operator. The full effect of the block in which this statement executes can easily be seen:

c:\@Work\Perl>perl -wMstrict -le
"my $rxExcl = do {
     my @excl = qw{ if else 1'b0 end };
     local $\" = q{^|};
     qr{(?x) (?: @excl ) \b};
     };
 print $rxExcl;
"
(?^:(?x) (?: if|else|1'b0|end ) \b)
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