Wabbajack ignores MO2 seperators and puts disabled mods at the bottom of the list in MO2

[VanStorm]

Describe the bug

I'm working on a collection for Cyberpunk 2077, and I am including multiple profiles. The different profiles enable or disable certain mods to account for different vram limitations on the users side.
When compiling the collection with Wabbajack the set order in MO2 gets ignored and the disabled mods get moved out of their categories (done via separators) to the bottom of the list (or when looking at the resulting modlist.txt at the top).
It should instead leave everything as is because that's the intended order by the creator of a collection.
I've attached the modlist.txt of one such profiles. Once the modlist_correct.txt which is how it's supposed to be and once the broken_modlist.txt which is what a user gets when installing the wabbajack collection.

It would be awesome if that could get addressed as it's a nuisance that currently keeps us from deploying the collection.

Additional Context

Win 11, Mod Organizer 2.5.2, Cyberpunk 2077

Wabbajack Version

4.2.1.3

Logs

Wabbajack.current.log

Modlist files:
modlist_correct.txt
modlist_broken.txt

[VanStorm]

Upon further investigation the issue seems to happen due to Wabbajack removing disabled mods from profiles, which then get added by MO2 at the bottom again. The only way around it is by manually setting all affected mods to "always_enabled".

It would be great if Wabbajack would cross reference across all included profiles before removing any mods from their respective modlist.txt files.