I think you are right. We should be able to negotiate the patent issues. Personally, I find the patenting of RUTF to be distasteful. You mentioned Mike Golden in an earlier post. As far as I am aware, he "gifted" his research. I find this commendable.
I also think that "local production" is a confusing term. What we have is a franchise system with limited suppliers. The risk is that we find ourselves at the mercy of a cartel in which a large proportion of income from production is "repatriated" to European companies.
I disagree about "standards". F75 and F100 are examples of evidence-based medicine developed over many years. The standard is a standard because it works. I do not think it impossibly hard or prohibitively expensive to meet the F100 standard and I think, for SAM at least, we should stick with that standard (until we have something that is both practicable and better). I think that Mark Manary's work in Malawi shows that local production of F100 RUTF is feasible.
WRT fortification. I think there may be problems with GAIN's approach of "large-scale" fortification as opposed to "mass" fortification. I am also concerned that selection of vehicles for fortification be driven by mass-production rather than by consumption so you may have (e.g.) wheat flour fortified because there are 2 or 3 mills producing it but rice is not fortified because production / distribution is decentralised when rice is the main staple. This is a species of "large-scale" vs. "mass" issue. GAIN are currently engaged in extensive M&E of their programs.
If we set aside the issues of "large-scale" vs. "mass" issue ... There is little doubt that universal fortification works. This is the predominant mode of intervention in many Western countries. For example, in the UK, non-dairy spreading fats (margarines) are fortified (this tends to target poorer households), table salt is iodised, bread / wheat flour is fortified, water is fluoridised (prevents dental caries). In many countries that I work in (Africa and Asia) mass distribution of vitamin A to children and mothers post-partum is the rule as is iron / folate supplements given free to pregnant women. Mass distribution of anti-helminthics is also common. This is a far more cost-effective approach than "supplement upon diagnosis" as diagnosis is only possible late in the deficiency, expensive, and may have limited coverage. With fortification of staples you exploit existing distribution structures and so simplify logistics. I have no idea why this is "sensitive" since it is standard practice.
Some degree of population-level targeting may be desirable in a large country such as India or Sudan. Then you would survey and fortify at regional levels. Even then it might be cheaper to fortify at the national level.