Well, while the clan has warriors genetically engineered to be small, the IS has dwarves, which I'm guessing have been at least mostly weeded out of the clan gene pool. IE, the clan wants every warrior, with the sole exceptions of proto pilots, to be physically imposing, but there's plenty of talent to recruit from in the is.
Problem is whether or not a dwarf will have the other required abilities to pilot a ProtoMech. There are a variety of medical conditions that can cause dwarfism, some of which would rule out a candidate immediately; piloting a ProtoMech is quite physically demanding.
Whether or not a given pilot is from the ASF phenotype, they still need to be able to handle some serious physical punishment in addition to the psychological and neurological issues that come with the job. ProtoMech fluff in TR: 3060 makes reference to the physical and mental demands of piloting a Proto and notes that ASF phenotypes are particularly well suited to the role.
Proto's have the same IS weight as 'Mechs using normal IS and while the fluff seems to suggest that Endo is involved somehow it doesn't state it outright. I was asking for a reason, but this might be an Ask the Lead Developer question, do Proto's use Endo-Steel and FF?
Per the design chapter intro from TM on p.77, they use a combination of Endo Steel and standard chassis materials. The Sphere cannot duplicate the technology by 3067, with the best available alternative too bulky to make up the difference. The armour used on ProtoMechs is only referred to as an alloy; Light Ferro-Fibrous is suggested as an option, but is stated to be both heavier and more bulky, to the point it would cause problems given the advantage of a ProtoMech lies in its size. The following page indicates that using Endo Steel (even their Mark II) or Ferro-Fibrous (even Light) will expand the ProtoMech's size to that of a normal 20-tonner.
The Sphere, with the information Sharon Bryan bought back from Huntress, expects to only be able to duplicate ProtoMech engines, heat sinks, and jump jets. Everything else is out of their reach, even if they get around the VDNI and pilot issue.
The Jihad won't exactly have helped their R&D efforts, especially since the facility from that text was captured by the Word of Blake.