I agree and have brought up this issue in the past as you linked to in your OP Some images don't lightbox? - #3 by piffy
The issue as I see it is that the “resized and lightboxed” settings are coupled.
Ideally I would like the resize settings to be similar to these defaults of 690x500px but the lightbox settings to be closer to 72x72px (like anything bigger than a large emoji or “sticker” sized image).
It seems like the primary intention of the lightbox is to view an unscaled version of the image but I definitely use it more as a carousel-style gallery. That’s why it’s a bit jarring when something 502px tall is treated differently from something 499px tall especially when they are in the same grid.