Firstly, this is about merging /bin, /sbin and /lib* into /usr. No one is suggesting that /var and /etc. should be merged. Let's stick to the real argument here.
Secondly, are you seriously suggesting the that performance of these rescue tools are constrained by their startup time due to the slowness of rotational media? And if performance is actually of such great importance, then what you really should be doing is, as has been suggested by Lennart, building them into a ramdisk, which is still much much faster than an SSD. Either way, "performance of system rescue" is not a compelling argument for such separation.