I haven't designed mods myself, but I've performed extensive mods on my HE-400, HE-560, and TH900, and have owned a modded T50RP (ZMF), and disagree.
On the contrary, I think most modders are doing what the engineers behind the headphones do themselves when they design the enclosure of the headphone--play around with materials, chamber dimensions, and other parameters until they achieved the desired tuning of the headphone. While not all modders have access to the sophisticated equipment headphone engineers use to tune equipment, they are pretty much performing the same process with their ears. Moreover, modders don't have to worry if their mods can be reproduced reliable in a factory at scale, or about the costs of the materials involved, so they can potentially better results with tuning than the headphones manufacturers.
The shelf-liner mod actually works really well with my HE-560. If it truly was sonically superior, it is entire conceivable that the Fostex Engineers decided not to do something like that for aesthetic or durability purposes.