Depends. If you can improve the sound and sell it for $100, why not?
Most of the reasons I can think of are economic. For starters, the site of design and site of manufacture are (often) in different countries these days, making simple mods and tweaks harder to implement efficiently. Something like changing the earpad design could be a lot more of a pain in the ass than you think, depending on the capabilities of a preferred component supplier. They would also likely want their cut for the cost of the change. This is why vertically integrated firms often have an advantage - they needn't pay the cost of profit to each supplier in (their) supply chain. Or, put more simply, outsourcing bad.
Also, a manufacturer may, with good reason, rather sell $20 phones in volume than $100 dollar phones in less quantities. On some level they understand "the market" and sensitivity to pricing at different levels. If you could get a $100 dollar sound WITHOUT incurring big production costs, a case can also be made to sell the "best" $20 dollar phone rather than one that will cost you for the added performance. Capturing market share by providing superior performance at a lower cost is the hallmark of innovative firms (even if profits are temporarily squeezed), with gouging to follow after competitors have been removed
. Then again that isn't always the case . . . .
My intuition is that manufacturers DO sweat the details seeking some sort of cost / performance outcome, but product cycles on many cheap headphones short (annual replacements), and are not necessarily driven by maximum sound quality. There is not a generational improvement on the same phones - instead they are replaced with a new model (I am thinking of, for example, the HD650 being replaced by the HD800). Also, the 'market' for headphones is not being driven by demand for maximum sound quality - if it were, people wouldn't be buying every pair of Beats being made over, say, the excellent-but-ugly Grados. Sales might be telling manufacturers that consumers want pretty plastic more than a 'flat' resonant-free sound. Honestly, most people I know that are uninitiated to the world of awesome hi-fi gear may try on my phones and say they "sound nice", but they don't go running out looking for the world's best phones afterward. They may miss my gear (when I take it away from them!), but they don't run out and buy it themselves. Straight up, good sound is my priority, it is not everyone else's.
There are so many examples I couldn't list them all. But just look at shoes in the shoe store - are they all "function" following "form"? I think not. Nike sells style, IMHO, while my ugly Brooks are the best dang running shoe I've ever worn. In computing, people "mod" by overclocking, yes, but the performance gains are consistently tiny compared to the risk of destroying/overheating components. Why bother? Auto-tuning: yes, there is more horsepower to be had - but what is the cost in long-term reliability? In contrast swapping out pads, cables, and playing with enclosures is not that risky and nice changes in sound quality can occur. I'm not saying I am all-for modding, but I do think anyone can play around and occasionally stumble on a worthwhile result. But what we can't do is re-invent the drivers as they are installed. I car auto, it is pretty common to have access to fantastic drivers that end up in Shi*** enclosures. Quality installations are critical to getting the most from them, but most of us lack the skills / nerve to do it (you would basically need custom enclosures and careful tuning). Hence the reason I'd almost prefer ponying up for the upgraded OEM systems and just live with the compromises rather than trying to best it. A lot of OEM systems lack dynamics and ultimate clarity, but the staging and frequency response are often better than what I can achieve.
TO MAKE A LONG STORY SHORT, I'd happily pay an extra $20-$50 dollars to have a manufacturer-modded version of the same headphone, to get good quality and to squeeze the last 10-20% of performance out of it. But I would not expect most people to be as committed to maximum performance as I. I would also prefer that, at the higher-end, manufacturers actually 'mod' phones as part of generational improvements each year. Auto companies do this all the time (improvements within product cycles), and since many flagship models stay on the market for years, interest could stay stoked by giving consumers new reasons to take a look.