It's better to think of the FM-Towns as a kind of general purpose arcade machine pressed into service as a Personal Computer. It just so happens that the CPU selected was x86 instead of something else (like a 68k or an SH-2 or ARM or something), so you could technically port IBM-PC compatible software to the system but with some additional caveats. As the x86 line of CPUs progressed, newer version of the FM-Towns came out to keep up (from the 386sx to the Pentium!), but somewhat like the Amiga in the West, the core specialized hardware more or less stayed the same.

1. The systems all came standard with a CD-ROM and expected to boot from this. They had no hard-drives. Writeable media was floppy disks.

2. Each CD-ROM had a copy of an entire OS on it. The relationship we think of today, where the OS is "installed" on the computer didn't exist with the FM-Towns. This meant that software might ship with an MS-DOS variant, a Windows 3.1 variant, or Fujitsu's own OS, whatever was necessary to run the software you were looking to use. There were ways to boot to the OS, and load things from CD-ROM, but this wasn't the primary way to boot the system for many users.

3. Memory map, peripherals, etc. were all different than an IBM-PC compatible. The BIOS was also unique to the system. This was because the graphics, sound, and other hardware was entirely different than IBM-PCs. Again, the system design was a ground up design where the CPU just so happened to be x86, there was no intention of being an IBM-PC compatible system in the design. This meant that IBM-PC compatible software had to be modified to support these differences.

4. They have an entirely custom video/audio subsystem that's entirely different from anything seen in the West on normal IBM-PCs. Lots of sprite-based support, smooth scrolling, the ability to run and overlay multiple resolution graphics with different priority levels (e.g. a high-res text mode could be place on top of a lower-res graphics mode). Keep in mind this was in 1988/89, when most home PCs were maybe EGA with some VGA, and very few even had accelerated mouse pointers in Windows.

* Audio was also completely different than anything on Western x86 systems of the time and would have blown away nearly anything on the Western markets for years. You had redbook audio, multiple PCM voices (better than an Amiga), digital real-time effects like echoes and filters, and multiple FM channels. Again, in 1988/89. IIR the audio hardware shared components used in actual high-end arcade games from that time.

As a result ports of high-end Japanese arcade games were pretty flawless, and there were some interesting ports from the West like a completely unique FM-Towns version of Lucas Arts' Loom that's far superior to pretty much every other port.

Here's some information on it. https://gekk.info/articles/towns-tour.html

EDIT: Here are some of the highlights:

• Towns OS had a custom GUI that was fairly advanced for the time.

• Towns OS included multimedia support.

• Towns OS had an API that provided advanced sound and graphics capabilities.

• Towns OS included support for overlaying videos in different modes, which boosted gaming and multimedia support.

• The FM Towns computers came standard with a mouse and gamepad in an era when PCs typically didn't have these things.