Amen to this. Having been a software maintainer myself (including in a large corporate setting), pristine upstream base-line + patches (as fine-grained as possible) are quite obviously the preferred form for maintaining corporately supported versions of free software projects. Anything else leads to significant inefficiencies and hair-pulling.
It used to be you'd check in actual tarball + patch files into an SCM (RedHat did this - perhaps still do; Sun did this with its SFW consolidation). However, current SCMs are now so good at examining history (git particularly) you can afford to check in the patched sources.
The interesting question then is, does that affect the preferred form requirement? If the patches used to be directly a source input to your build process (and hence clearly covered by the GPL), if having access to those patches is important to be able to maintain (i.e. modify further) that code base, if then by some technicality the build process no longer works on the patches to what extent are the patches no longer preferred for the purposes of the GPL?