There seems to be a blurring of the line between tweaking and modification these days.
Replacing caps, resistors, wire, pots, etc. is just tweaking what's already there. Posts regarding this discussion can be pretty frustrating, as very few people have sat down and listened to many different parts in the same circuit (For good reasons - it takes a long time and can get expensive), so it becomes people just recommending whatever they decided to use on their last build.
An actual modification is more about changing how the amp operates. One example is Xavier tweaking the BeePre to get the 6A3 to operate properly. Another good example is when I worked with Chris to modify his Crack to run 5687's.
Link Paul Joppa is perhaps the most prolific mentor in this regard, leading to a lot of all directly heated and shunt regulated amps, as well as some crazy creations hidden away at BHQ. The funny thing about this is that these modifications generally cost
a ton less than putting boutique parts into your amplifier, and there will absolutely be a difference. (I'm still thinking about making a 1626 Stereomour)