Linux Port Not Saving With Custom Content Loaded

I really didn't want to register again over it, (I did have an old account from 2009, but I lost the old email it's linked too.) but this issue is really bugging me, so I'm asking for a few pointers here.

Pretty much, I fully migrated to Ubuntu on a new hard drive recently, and I have successfully reinstalled everything I need, including compiling the drivers for my brand new Wacom tablet. (Took me three days, but I did it!) All my favorite games are good to go too, excect SRB2.

I don't have access to the Windows version of the game on this drive, and with SRB2 refusing to save progress of any kind when custom content is loaded, it's killing my enjoyment of the game, since I play as Hinote constantly. I can't play a level, save, and go back to it later. I don't have hours of time to marathon the Mystic Realm in one sitting like I used to.

Why is it doing this? Is it a permissions issue? Is there a line in the source code I can uncomment to remove the content check? I never really cared for online play since analog control wasn't a possibility, so it doesn't matter to me if a patched build doesn't cooperate in net games. I just want to play Tortured Planet and the normal game as Hinote without losing all my progress.

This is intentional, and happens in all versions of the game. In fact, the game even gives a console warning when you load the file telling you that the game won't record statistics until the game is restarted. There are two main reasons:

1. The save files in SRB2 don't actually know what files you have loaded at all. Hence, the game would act weird if you played as a custom character, saved, and then tried to load that save later without loading that character. Even worse, the game treats characters by the order added, not name, so if you added two characters A and B in that order, saved a game playing as A, and then reloaded later adding B first, the game would load up the game as B. There are a ton of similar loading issues when saving with other kinds of custom content loaded.
2. The game also treats mods as "cheats" in basically every way but name. Adding a file triggers the modified flag, making the game stop saving everything (even game time) until the game is restarted. This is a basic check to make it harder to cheat at the game by doing something like making a WAD that has all seven emeralds, saving, and then loading that save in the unmodified game.

In case you're wondering, mods that DO save do so via custom save data in their config, and that save is completely separate from the main game's save data. You could probably disable these checks pretty easily by editing the code, but honestly, you could also just use the MAP command to level select since the game thinks you're cheating anyways, and that would be way easier.

All of that, I've long since known, so I keep custom content loaded through the autoconfig file to prevent conflicts in save files. The list of stuff I keep loaded is rather scarce these days, it's just Hinote and a music replacement wad for the title screen; the main game has had enough content to stand on its own since 2.0 was released.

However, the Windows version of the game has always saved progress in mods to their own files, and I am at a loss to understand why the Linux port isn't doing this as well. I've pinned it down to an error in the log.

Which I'm failing to understand why it's not saving progress, when it can read and write any other kind of file to the .srb2 directory in my /home folder without issue.