There is one way to avoid the graphical problem. Well two actually, but both will have an impact on playability.
One way is to use non transparent room sprites, or put "carpets" in rooms. This will make the strips almost impossible to see and will affect the way the player deals with airless rooms. It's not ideal but it can work.
You don't necessarily need to fill the entire room either. As long as you know where the low-oxy stripes end, you can paint machinery, carpets, whatever over the part that is missing the strips and hide the fact. This will only work for system rooms since you cannot paint empty rooms. Even then, it may be possible to stick a "fake" system in a empty room, and paint that. Extra work for sure, but can be pulled off if the ship simply must have a non standard size room.
Another way is to replace the stripes with blank images. This removes them entirely so the mod will play like pre-1.03.1 FTL with the rooms turning pink only. It will again affect the playability and is probably the worst solution but i'm throwing it here as an option.