This wasn't the solution I was hoping for in the context of how I posed the question but I found a workaround for anyone else that runs into this:
Instead of using system('cmd') where cmd is the Perl script call and arguments, use system('yes | cmd'). This automatically provides affirmative answers to proceed through any yes/no prompts. More complex promps and responses can be passed in with files containing 'expect' and 'send' however this is all I needed for my purposes.
Still not sure if MATLAB can monitor its own command window this way but Linux is capable of handling it via the command line so feed that into the system function