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A Mac SE upgraded with a third-party '030 accelerator is still different from an official Apple SE/30 in several ways. Some differences are minor, but some may be important:
Video. When the Mac SE updates the screen, other activity stops, but the SE/30 can access RAM to update the screen while the CPU continues with other tasks. If you're using the built-in 9-inch screen, you won't care about this difference. But if you are using a much larger screen with an accelerated SE, screen updates may be slightly slower than they would be on an SE/30 with the same monitor. More significantly, an SE's external monitor options are limited to black-and-white or a mere eight colors.
Sound. The SE/30 uses hardware to handle much of the sound processing performed by software on an SE running System 6. Heavy use of sound on an SE, even with an accelerator board installed, can significantly slow down other activities, while on an SE/30 it will have less of an effect. Also, the headphone jack on the SE is not stereo like the SE/30's.
SCSI. Although the standard wisdom is that hard disk drives used with the Mac SE should be initialized with a 2:1 interleave, many work with a 1:1 interleave on any Mac. An accelerator board doesn't change this. If you have a drive with a 2:1 interleave connected to an accelerated SE, you could reinitialize the drive to 1:1 and get a minor performance benefit. However, if your work requires continuous, heavy disk access, you may experience worse performance with an accelerated SE and a 1:1 drive than with an SE/30.
Floppy. The Mac SE/30 has Apple's SuperDrive; an accelerated SE retains the standard 800-Kbyte floppy drive. Third-party products that perform the same functions as the SuperDrive are available.
Memory. Memory management is more limited on an SE than on more-recent Macs, and that could be ...