One of the problems with patching security holes is that the bad guys can compare two recent versions, discover the change and create an exploit (in some cases automatically). If a victim is not using the latest version of the software, then they're toast.
Normally, a compiler will optimize a program/library for space or speed. If, however, the optimizer included randomized register assignments, conditional ordering, selection of optimizations, etc.; then new versions would have huge numbers of changes from older ones and analysis of the change would be much more complicated and expensive.
With sufficient work, automated comparisons of differently optimized code may be possible, but this is a long way off.
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Clever! And just a little such variation would do the job, at least for three years, and give the defense some breathing time.
You have stumbled upon an area of much research in the field of reversing. Generally speaking, it's a tough task to do but it's even harder to reverse.
What I believe would help more is if your compiler could produce several value flow controls using some modules that are real and necessary but also using some modules that are fake and do only similar items. The key would be that they must be valid controls of flow, or at least ones that take a long time to terminate.
Static code analysis on the resulting binaries would be much more difficult in this manner, but I support your efforts.