The point is that there are usually more efficient ways to accomplish what those peripherals do. Especially using I/O efficient interfaces like I2S etc. That usually also does away with any messy voltage level conversion in massive parallel arrays. Direct connection to the FPGA also imply the risk to fry the main chip.
You can do messy line interfacing and use lots of I/O to connect a sampler. Or you could use a small chip that does it all directly. Just because something is possible doesn't make it the right solution.
Oh, I agree with you totally, it makes a lot more sense to build some new custom hardware replace whatever external devices you might have on the serial & parallel ports. But there is the software involved. If it were relatively easy to do the Amiga's ports, then you wouldn't have to write a new sampler program for example.
Baud is signaling rate, bits per cycle. The bit rate is possible either by dividing some other clock or by using a PLL (DCM). It might require a update to the FPGA binary (core) however.
That's what I meant to say. To drive the Miracle piano, the FPGA core would have to hit the MIDI bit rate. I guess that would depend on the design of that core.