I remember a BASIC program I used once to dump my DPC-300 ROMs to a floppy, someone sent it on the MSX Mailing List ages ago...I think I still have it somewhere, but, again, I can't use it, because my TPC-310 doesn't work...
I think one problem with dumping PROMs directly is that on hw level you can f.e. connect data or address lines differently, say, D0 from ROM to D8 on MSX bus and vice versa and then modify the ROM data accordingly as well swapping bits - this makes it work on the hardware but content of direct read and read via MSX would be different. IIRC there were some cases when it was donle like that (some IDE interface or so, don't remember exactly which device)
Pesadelo was made like that.
More often than not, this is done to simplify the PCB. If you consider the ROM maker's bit numbers as just labels and not actual bits, you can shuffle them as convenient to make PCB routing easier. This was done among others with Shadow of the Unicorn for the Spectrum, the PCB is single-faced and does not have a single bridge thanks to this trick. I haven't analysed the Pesadelo PCB, but I bet it was done for routing simplification as well.
