Yes, that's a limitation of trying to ensure exact binary reconstruction. Luckily there is also a separate line of work on detecting the compiler version and optimization flags based on a binary – it turns out this is not that hard and it's easy to get a bunch of labeled data for a classifier.

If folks are interested in reading more there's a nice paper by Grammatech on the idea: https://eschulte.github.io/data/bed.pdf (though it's pre-LLM and uses evolutionary algorithms on the initial decompilation to search for a version that recompiles exactly).