You can find examples of this type of thing all over the place, but a notable one is with the Apache Web server. When compiling, there is a program called apaci which is a wrapper that works just like you want. It is simply a sh script. Here's a theoretical approximation:

#!/bin/sh

# Set Variables
FOO="bar"
CC="gcc"
COPTS="-l -q -r"

# Execute whatever
$*
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All it does is set a few variables and then run whatever commands you give it. This also means that make doesn't "talk" as much during compiles since the commands are shorter. I'm not a fan of Makefiles which spew out reams of useless "-I../../../../../src -DSOMETHING -DSOMETHING_ELSE ..." type parameters since it is harder to casually spot warnings, and harder still to parse what is actually going on.

As a note, though, you may not want to use Perl to actually execute the make process(es) as it is fairly heavy compared to a shell, something that might slow down your build. It might be advantageous for Perl to generate the required shell scripts and then kick off the whole process with a single exec call.