I won't claim to clearly understand what you are doing but it looks like using (?{...}) is an overly complex way to go here. Something much simpler might work for you:

s/(...)/ func( $1 ) || $1 /ge;

s/(\[(...)\])/ func( $2 ) || $1 /ge;

s/(\[(...)\])/
    my $ret= func( $2 );
    defined $ret ? "[$ret]" : $1
/ge;

s/(\[(...)\])/
    my @ret= func( $2 );
    @ret ? "[@ret]" : $1;
/ge;
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