[thefreeman]

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.

[wvenable]

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.