He's not just referring to a jailbroken phone. From what I gather, the main purpose of Substrate is to allow apps to monkey patch functionality in other apps. I can see how this could be frustrating if users report issues that are actually caused by another app "hacking" the reported app.
The primary purpose of jailbreaking your phone is to run tweaks that use MobileSubstrate. I think Saurik himself has said Cydia only contains a handful of "apps" everything else is a tweak.
Unless the author has written an app badly in need of a tweak specifically targeting it, I doubt it's being patched directly.