I've finally been able to listen to the 5.1 version on my sound system. The low volume level issues I was having earlier don't seem to apply when the file is played in its native format; I was about three-quarters convinced of that already, but having looked at the waveform and listened in 5.1 mode I'm now certain that there is no DRC as I had feared. The average volume is the same too, so no dialnorm or anything like that going on. A very small amount of clipping occasionally occurs in the center channel on the highest peak volumes, but like the clipping I documented earlier in the '93 source, it is very brief and quite inaudible.
For whatever reason, when playing the file in VLC via headphones (which was all I could do away from home), the volume was substantially reduced, but during proper 5.1 playback this does not occur. Add that to the potential phase issues that may arise when downmixing something that has already been upmixed, and I will add the caveat that this 5.1 mix ought not to be played without a 5.1 system. For ideal results the stereo version should be used if such a system is not available.
Though the problems I thought were present turned out to be a false alarm, in the course of listening to the 5.1 file I discovered another issue, one which I confess has me somewhat baffled. I made only brief mention of it earlier in this thread, but on a few occasions I used the bass effects from the 1993 mix for the LFE channel, isolating them from the rest of the mix and adjusting to an appropriate volume, in short amplifying what was already present in the '93 mix. On my 2.1 AC3 encode, they sound the way I wanted them to sound, but on the 5.1, they seem by varying degrees to be subdued, being only marginally louder than the '93 if at all. I don't know what is causing this discrepancy.
I have heard that AC3 encoding, being lossy in nature, may alter the phase relationships between the channels, so that what should blend together becomes less coherent. The likelihood that this would occur with the LFE channel is greater, because lossy encoding generally devotes more of its bandwidth to the midrange, where human hearing is the most sensitive, and less to the high and low frequencies. Bass frequencies are also more likely to interact with each other and their acoustic environment in anomalous ways. But I can't say specifically what is causing this problem in the mix--whether it is the lossy encode of duplicated bass, or whether the upmixing caused some cancellation, or even if my receiver is simply processing the two versions differently. The reason I used a few '93 bass effects was because I felt that neither special edition worked as well for those sounds, but it looks like I'm going to have to make the SE bass work if I want it to sound right. Should have realised something like this could happen, but it's an area that is really beyond my knowledge, since I am not a trained professional. Blast . . .
I don't think anyone but me would have noticed the discrepancy, since I'm the one who put this thing together (and my subwoofer is of higher fidelity than what many people generally own, indeed it is probably the highest quality component in my system), but I want this to sound as good as I can make it. Hopefully it won't take long to fix.