While its true that engine components are designed to optimize their efficiency for the cruise condition to give best overall SFC, SAR etc. The over-riding reason that the efficiency is best at altitude is down to the fact that the cycle efficiency for gas turbines is a function of overall temperature ratio.
Maximum cycle temperature is fixed by HP turbine and NGV material and cooling limits, but the minimum is governed by ambient temperature and thus altitude (upto the tropopause at least).
So High Altitude = High Temperature Ratio