There should be less troubles with Tools in the future. The tools site is getting overhauled. Some work done on auto-updates AFAIK.
The reason Autoseek is not enabled for all samples is that it is very processor intensive and time consuming. This was explained on July 2010 in this post by sharevari (the creator of the feature).
Because of this, I don’t forsee your feature request making it into the core product. Disallowing was a design decision.
With the power of scripting, however, you can do what you want 