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I cannot reproduce, and --single-instance has absolutely nothing to do with other options. Presumably you have another kitty -1 instance running which has macos_option_as_alt set to no and your subsequent invocations are opening new windows in that instance. Remember that all subsequent invocation using --single-instance use the same options as the oiginal invocation (as long as the original is still running).
None of my kitty config has that option set to no. It's even explicitly set to yes.
It's odd because the original instance (and I made sure it was the only running instance with ps aux) respects alt, and so do new instances opened with kitty. But if I open a new window with kitty -1, the new window's option key is not treated as alt.