I did not check, but most probably a new GCC version is installed with this version. This might do different optimizations, and code generation, so it will produce different output.
Also, Cypress might have changed the way how they do component placement and routing to produce better results. This also affects the output.
Thanks for the reply, I also believe the latter in your email to be correct. Building two projects without any components in Creator 3.3SP2 and 4.0 yields the same binary file.
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The placement and routing algorithm is updated.