If you want to carry those stage modifications to a X6 Tweaks build, you could theorically do it manually by replacing data from stage files.
If you manage to identify those files within the DAT file, you can even do the replacements without having to unpack/repack it.
For that, I would take the addresses of the DAT file from the original game as a reference (https://pastebin.com/Z94UYPM9
), and by taking sample data from the start/end of each file, locate the stage files within the DAT files of both X6 Tweaks and the other hack.
Same for any other changes (damage tables on the PS-EXE, for example). The X6 Tweaks documentation should cover all the relevant addresses.
Modifying the other way around (start from the other hack, and try to run it on the X6 Tweaks Patcher) will never work. The patcher is hardcoded to work on a clean build.
(I'm not gonna work on this.)