Ok, after some huge research, I managed to find quite a good solution to this.
The problem exists because our dearest Microsoft (who even asked them to! -.-) changed the way sound card drivers work in Vista/7/8. The systems no longer support analog audio at all, so it's all handled digitally (on a sidenote, lack of EAX support on those systems also comes from this change). This is why lowering audio cd volume in old games does nothing.
But, I recently learned that DOSBox can cap the audio volume internally if the CD image is in .cue/.bin format. Here's how it works.
For this method, I'm using my prepared game CD, with fully restored audio tracks (they are played properly when they should be, because the triggers were never removed in the PC version, despite the tracks weren't included on the disc). It is important that the image is in .cue/.bin format, because DOSBox can adjust the audio volume only when a .cue file exists (.iso/.nrg/.mds will not work). I'm NOT mounting it at all (neither in DAEMON tools nor in a physical drive), and I'm just using DOSBox's imgmount command instead.
So, to use imgmount, I edited the dosbox.conf file in Glidos directory, and added the following lines:
imgmount d "d:\CD_location\CDimg.cue" -t iso -fs iso
mixer cdaudio 50:50
Finally, I set Glidos's audio settings to None, so that DOSBox handles audio tracks.
The two values after cdaudio control the volume of the left/right audio channel, in percentages. I found that 50% on both right/left channel works just great for me. So even though changing the volume in-game still does nothing, the audio volume is capped permanently on my desired level. Hooray, my ear drums are safe now.
Whew, that was quite some wall 'o' text. Now please excuse me, it's time for an all-nighter marathon of geeking TR1 with beautifully working audio and great Glidos graphics. *me gusta face*