Just don't use smartmatch... And if files are small, I don't see any reason to read them byte by byte.

$ perl -0777 -nE '
    my $count = 0;
    $count += length $2 while /(.)(\1+)/g;
    say $count;
' <<< "1112223333"
7

$ perldoc perlop | perl -0777 -nE '
    my $count = 0;
    $count += length $2 while /(.)(\1+)/g;
    say $count;
'
22788
[download]

(just don't decode your strings, and you'll have bytes... pretty much)