shouldn't the company that designed it have thought of such simple things?

You could ask why companies ever make and release really bad products. It isn't doubted that they do, so I don't doubt that they also make some good products that not as good as they could be

This is what I don't get... Why seemingly-proven mods are not taken on board by those companies and incorporated in the design evolution?

... Why seemingly-proven mods are not taken on board by those companies and incorporated in the design evolution?

Aesthetics could be one reason. And who knows what definitions of neutrality are in the various design houses?

And some of the mods are very elaborate, so they can't possibly incorporate it into their production line without significantly increasing cost. Some of these manufacturers (Sennheiser, Beyerdynamic, AKG, etc...) make more than just headphones after all, so their focus is not solely on headphones.

I can partly answer this question, as I see it being in the rather small headphone company.

So, if we are talking about expensive stuff...
You need to create headphone that is both pleasing visually, light, comfy to wear, fit in target MSRP and be acoustically ideal for a specific transducer. Its good if you have ready sample of this transducer at hand, but it can be also in the work by the time housing is designed. And even if you know specs it will have, they can change at the end. So, you will need to meet those criteria, keeping in mind that, very often, they are contradictory to each other.
Good if you can have your time, but usually there is kind of a deadline.
In the ideal world, you can design it step-by-step. But reality isnt ideal, and sometimes you need to re-plan and re-do the work. And in a worse scenario, you already payed money to contractor, they completed their part, and bam, plans changed, you need to do it again. Meaning, paying again for the same thing, meaning increased MSRP, meaning you may require further changes to justify increased price. Or, you accept it as is, or find another way to correct it.
Say, you have an unplanned resonance. As every modder knows, you can damp it. So you will need...

1. To find a material that fits and do its job. May take some time.
2. Find it for reasonable money. Like, buying something for $10 to do single mod at home is one thing. Adding $10 to base cost is another. $10 base cost can easily translate to $100 msrp increase, or even more, depending on country.
3. Find a way to cut it relatively fast and even. Like, many woven materials dont like laser cutting. And its not easy to find cutting machine suitable for woven fabrics. Sure, you always can hire some man who will sit down the whole day and carefully cut it with a knife. But, dont forget to add their salary to the raw cost as well.
Yea, there are materials commonly used for this, which dont have such problems with production, but they can, and often is, less than optimal.
4. Carefully glue it to its place. Sound simple, but there may be a lot of pitfalls, like choosing the right glue, which will not damage housing or material, will be easy to apply to a specific place ("human factor" plays it role), be not toxic, etc..
At the very least, it will take time. Deadline, remember. But most likely it will be worse - take time, raise base cost and complicating production process which is both - more time and more money.

So here is the decisions company need to make - change deadline, invest additional resources, or just leave this damn thing be. Which will hurt more? This all must be calculated and taken into account.

And here I'm talking just about production, not taking into account marketing.. Maybe that sound was intended at the beginning. Maybe it is planned to release "new and improved" model later.
Of course, as you said, possibly engineer just miss the point at all. But, if we are talking about flaws easily seen on measurements, I would not expect this to be the case.

Simply put - sometimes work, that can be done home in 5 minutes and ten bucks, will take weeks and thousands of dollars in mass production.

Modding is not exclusive to only headphones. Far from it.

Then of course there are those mods that are simply ahead of their time...