I think I understand your way of thinking and agree that within the syllabus of any martial art we can find techniques that may not be the best solution for self-defense. For example I have seen an Aikikai shihan in a official Embu, he does techniques where he twirl his Uke around him like a merry-go-round, for about a minute. Nice for demo, but try that against straatjongens (streetfighters) here in Jakarta, and I am sure the shihan will be introduced to the concept of "early retirement".
I am a huge fan of Tomiki Aikido, but within the Koryu Goshin no Kata I have seen technique where Tomiki Shihan does a single leg takedown against a knife-wielding opponent without trying to secure the knife hand first. It's a good technique against non-knife-fighters, but against an arnis Master, even Tomiki shihan himself will find himself at a severe disadvantage.
Hell, even in my own Dentokan version of Hakko-ryu, I can find techniques that are not 100% perfect for self-defense. Most of the Aiki Nage type techniques on Shodan-Gi (for example Kubishime Dori and Ushiro Zemi Otoshi) are done without gripping Uke. In the real world, when a straatjongen sensed that we are about to break his balance, he will let go of his grip and punch us in the head immediately. So, in reality situations I think we have to counter-grip or at least apply atemi before moving to any type of aiki nage.