In short: yes, there is a way third-party plugins can hook in to add theme options. Still needs a bit more work. I will be in touch this coming week to get you some more info.
Happy New Year!
P.S. Re: the undefined index error, that’s probably a situation where we should be calling isset before trying to access an option array key. As per this thread, the mPDF exporter hasn’t been updated much of late.