I have a feeling that you are overcomplicating things (either that, or asking the wrong question). Using PK3 is actually straight forward, and doesn't require any special tools. When I learned how to do it, I just followed the rules laid out on this page:
https://zdoom.org/wiki/Using_ZIPs_as_WAD_replacement
As you can see from that page, it's the directory structure inside the PK3 that is really important, but it's also pretty simple. If you know you want to include some sounds, you drop files of an appropriate format into a sounds folder and write a SNDINFO.txt file for them that stays in the root of the PK3. If you want textures, it's even simpler - drop files of an appropriate format (e.g. png) into a textures folder. Sprites go in a sprites folder (again, an appropriate format - such as png - is required, and you will also want to set sprite offsets (which Slade is good at)). Want to replace the titlepic? stick your replacement in a graphics folder. Got an MP3 that you want to use? Give it a suitable name and stick it in the music folder (and possibly reference it in a MAPINFO lump if needed). etc. etc.
What I'm trying to get at, it that there really isn't anything magical about PK3 files. It's just a case of putting the resources in the right place so that the game and control files know where to look for them. To be fair, much of the time, the same thing applies for WAD files too. Put the right kind of resources into the correct namespace. The difference is that the WAD format requires a special tool to do it, and there are no folders, so you have to create "markers" in the file like S_START and S_END which basically means "everything between these markers should be treated as a sprite".
In fact, when working with files for the PK3 structure, you don't even need to put them into a PK3 file. If you have a folder on your computer that has the same directory structure as a PK3, you can load the folder and it will work - provided all the data is in the right place and the right format. To me, that's the real advantage of PK3 files. They require very little in the way of specialist tools. You set up a nice neat folder structure on your PC, with sub-folders and pngs, oggs, txt files and so on in it, and then zip everything up into a single file for convenience. Compare that to a WAD file which is an arcane format, created for a need that existed in 1993, which requires specialist tools, and marker lumps to group like items together because it doesn't support internal folders.
