I've manually replaced the musical instrument patches (but not the percussion ones) with the DMXOPL ones from the Freedoom repo. Turns out I needed to use the variants with the -2 suffix at the end, because the default ones sound very off in MBF. I'm not sure if this is the intended or best quality, but at least the songs sound recognizable in the port. (I wonder if this works at all on real hardware? I only run MBF in DOSBox.)
I also tried out newer DMXOPL releases from the project's GitHub page, not in the least because I can convert the whole .op2 file into .IBK in OPL3BankEditor, instead of individually replacing instrument files. However, what I tested so far (v2.11d and v2.10) sounds incredibly off in MBF.
UPD: Alright, I figured out a few things. First, OPL3BankEditor can load whole GENMIDI lumps if they have the .op2 extension, which made testing easier. Second, I realised that both the Freedoom GENMIDI lump and the recent releases of DMXOPL v2.x actually contain more data per each instrument than IBK can store, namely Carrier 2 and Modulator 2 sets of values, while IBK can only recognize Carrier 1 and Modulator 1. It appears that when banks with twin carriers and modulators are imported, half of them is truncated, and this causes the instruments to sound off in MBF.
With this in mind, I went back to DMXOPL v1.11, which is the latest to only have Carrier 1 and Modulator 1, and quickly converted it into IBK, which I'm attaching below as DMXOPL11.IBK. I think is sounds pretty decent in-game, and certainly an improvement over the default instrument setup.