I think that the FAR believed that the life they spread throughout the universe would continue and they wanted to try to give them the best chances they could, possibly past their own existence. Just as Eva-01 will be sign that humans have lived, so shall it be a sign the FAR lived as well.
Regarding Shinji, I still believe Instrumentality is locally based. Yes, Rei/Lilith/Adam obtained god-like powers but if they had god-like powers so did every other Seed on every other seeded planet. I believe that the power Rei wielded was only localized on her own seeded planet and not any others. After all, every time she traversed time she was only able to have a Rei ghost show up to stare at Shinji for a few seconds before disappearing promptly. Not exactly the most powerful example of space-time manipulation I've seen. It makes perfect sense that Instrumentality is only localized to the planet of their seed, at least to me. I'm pretty sure the FAR did want Instrumentality, however. Instrumentality was specifically mentioned in the Dead Sea Scrolls so the FAR evidently expected it to happen or at least saw it as a possible outcome. What Instrumentality actually is is a forced evolution of the species into a higher order of existence. It just so happens that for humans that entails fusing everyone together into goo. :/ That seems pretty bad to us as an individualistic species but on the grand scale of things evolution is a good thing but only if they are ready. As such, it makes more sense to me that Instrumentality is a localized thing, for when a species reaches a certain plateau and thus is "rewarded" with ascension. The reason I think Shinji was able to escape Instrumentality after the fact was because Rei gave him special treatment during the whole process. She asked him whether he wanted to become one with everyone and he said no, allowing him to return to his own existence and free himself, thereby giving everyone else the ability to as well.
This is just what I've interpreted on my own and from the evageeks wiki, however. It may be that you're right and the FAR didn't want Instrumentality to occur and merely mentioned it as a possibility, actually wanting species to evolve naturally rather than through evolution.