OS4.1 doesn't support classic games that shut down the OS, so they simply won't work. 4.1FE does ship with UAE integrated, so you can run classic games in an emulator within OS 4.1 by double-clicking it, but if you're emulating a classic (or running on a real classic), it's probably a lot easier and faster to create a dual-boot setup running OS 3.
Running games from floppy (ADF) should still work fine however, since booting from cold the classic is still in OS 3 / 68k mode, and when it detects the floppy it will boot from that instead of the hard drive.
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