They did do exactly that in many cases - the ES systems were not transistor-by-transistor copies of the IBM systems. The original article (PDF link) has a lette

They did do exactly that in many cases - the ES systems were not transistor-by-transistor copies of the IBM systems. The original article (PDF link) has a letter from Andrei Gagarin which mentions that the ES1065 had entirely original hardware design and architecture (while presumably being ISA-compatible with the IBM systems). Also, not all ES systems were IBM 360 compatible - the ES project was an overall scheme for improving and modernizing the computer industry of the Socialist block (the name ES was in fact created when Bulgaria, Czechoslovakia, Hungary and other countries joined the project, which grew out of a USSR-only project called "Ryad"), and although the IBM 360 architecture was central to ES, there were completely incompatible systems in the ES line.