It really does appear that the early HE-5s had production variation problems. The example I heard at the local meet in Feb had wonderful bass.
Rule of thumb: the best results from a modding adventure will most likely be had from a headphone that's very bassy in stock form. This indicates the driver is tuned low. Modding will change the tuning upward, so you want to start as low as possible. The YH-100 is not much different from its Ortho brethren with one exception: it's tuned much lower. Some, not all, HP-3s and HP-50s are tuned almost as low.
So in that sense, yes, it's something innate, since driver tuning is set at the factory. This is true of the HE-5 as well and is directly related to its diaphragm mass and tension. Getting consistent tension in mass production is not trivial, so we shouldn't be surprised to hear stories of differing sounds from a startup model. I suspect the early high retail price of Yamaha's Orthos was due to the difficulty of getting consistent quality in production-- and the first-gen Orthos weren't even tensioned.
And yes, bending the metal headband ever so gently in small steps is the key to getting the right clamping force.