I have the answer! (And sorry for necroposting, but every time I myself have wanted to change this, Google brings me to this forum topic. It finally annoyed me enough to dive in and fix it myself.)
The answer lies in the Pak.zip file, as you might imagine. The steps:
1. From directly within Pak.zip's "media" folder, extract the file "massfile.dat.ADM" somewhere conventient, such as your Desktop.
2. Use the very useful ADM <-> DAT converter (Full credit to its author, you did a fantastic job making this! - Link to original topic here
) to convert this .adm file to its human-readable .dat form.
3. Delete massfile.dat.adm from the location you extracted it to. Here's why: Now that you've converted it to .dat, you don't need it anymore. You'll be creating a new one later on from your modified data, and it's THAT copy of this file that you'll be using. Best to delete this one so you know you're working with your custom data later.
4. Search the newly created massfile.dat file for this text string: [MEDIA/DUNGEONS/MAIN.DAT]
5. Edit this data (or replace it completely using data from, say, The Little Horde mod) to reflect how you want the Main Dungeon to behave. As an example I'll provide the first few lines from mine:
etc etc. Note the MUCH harder level matching of Player's level * 1.5, minimum of 4 champions, max of 20 on this floor, and increased monsters per meter!
Note also: Every "STRATA" (up to 34, from memory) needs to be individually edited depending on how many champions you want, how many monsters should be everywhere, etc etc.
A nice caveat: You can also simply remove any line containing "MONSTER_LEVEL_MIN" and "MONSTER_LEVEL_MAX" which are normally responsible for strangling the monster levels. You don't need to modify each of them to be minimum of 1 and maximum of whatever; deleting those lines entirely is more efficient.
6. Use the converter tool to convert your now-custom "massfile.dat" back to "massfile.dat.adm" format.
7. Overwrite the existing file in Pak.zip's "media" folder with your newly converted, modified copy.
It seems that the contents of "massfile.dat.adm" inside Pak.zip take absolute priority over any mods when it comes to the main dungeon, but it allows itself to be overridden when it comes to the other optional dungeons. Odd, but not unbeatable.
I myself have tested this by creating a completely new character, making him level 6 via character editor, THEN heading into the main dungeon. I immediately ran into Level 7 enemies instead of the normally-expected level 1 ones. Success!