Even small IC can contain large bulk of redstone logic and it full emulation can take a lot of server resources, especially at large servers. Maybe this can be improved via compiling logic into specific bytecode ?

Furthermore, any redstone circut can be translated into system of boolean equations, and this system always can be solved. So, why repeat the extra steps if the relation between input and output signal can be received clearly ?

For example, IC 64x64 can contain 1024 (!) independent clock-generator, that almost certainly will lead to server performance glitch.

I think you are underestimating just how much time it would take to compile something like this, especially if you are using 64 different io pins with hundreds of time-dependent gates.

Logic only containing combinational logic can be converted to equations. Gates such as timers are too complex to compile.

The system will be optimized as time goes on, but I don't have a way to compile it into anything.

Yes, you can convert anything on circuit, except timers. But even timers and other element with delay can be simplifed usuing time-dependent Heaviside function.

The result is relative-time depend solution of equation system, where all state switch time point can be received clearly.

I think that this is the only way to build complex circuits in the "real world", in running server

If you have some insight how this could be done, by all means.

I'd be willing to tackle this problem

Bitcoin miner written in verilog, compiled in about 5 seconds.

This process can be transferred in separate thread/pool, while manufacturing in-game IC.