I see two possible solutions:

1. Although you cannot change the files, nobody says you have to use them "as is": you could pre-process them and turn them into a more workable data-format and then work with this data; or
2. You could write a subroutine that takes two arguments: the first is the <name> and the second is the %<name>Cmd hash:

   sub process {
       my ($name, %Cmd) = @_;
   
       $ApidOffset = $Application{$name}{AppApidOffset};
       
       foreach $cmd (keys %Cmd) {
           if (int($fssbCmd{$cmd}{fixed_pattern}) <= 15) {
           $opcode = sprintf("0%x",$Cmd{$cmd}{fixed_pattern});
           } else {
           $opcode = sprintf("%x",$Cmd{$cmd}{fixed_pattern});
           }
           $apid = sprintf("%x",$ApidBase+$ApidOffset);
           $cmdData{$cmd} = {opcode => "0x$opcode", apid => "0x$apid"};
       };
   }
   [download]

   Of course you will still have 11 subroutine calls to make, but I think you can survive that!

Update: fixed a typo in the subroutine (%Cmd instead of %cmd)