Just to clear up any confusion (or perhaps add more), S01 video originates from a Beatrice-Raws release which the encoder Urotsuki states the video is actually an upscale from ~540 (https://nyaa.si/view/1063605#com-5) but that doesn't directly explain why the videos have 2 different heights. This is mere speculation but perhaps deinterlacing may have resulted in the strange resolutions or some mistake occurred during encoding. Considering the first season was released in 2003, there would be no HD or even Full HD resolution available.

We try to use the "original" resolution whenever possible but in this case it seems our source ended up using an upscaled S01. If a better source existed at ~540p, we would prefer to use that instead as it portrays essentially the same image with less data. Regardless, we are satisfied with Gunslinger Girl Season 1, strange resolutions and all. As a fun fact, this was our first encode to correctly use this much photon-noise and also apply photon-noise to the chroma plane to achieve a similar grain to the source.

Thanks for checking out our release,
-Sav1or