The main reason is spectral sensitivity. Many older black-and-white films were much more sensitive to blue/violet light than to red light, and early films were sometimes effectively "blue sensitive" rather than truly panchromatic. That means blue areas exposed the film more strongly and reproduced as lighter gray, while red areas often came out much darker.

Even with panchromatic film, a colored filter on the lens could further change tonal rendering. A blue filter would pass blue light and suppress red more strongly, making blue subjects lighter and red ones darker in the final image.

A modern digital black-and-white conversion usually starts from a full-color capture and then maps RGB channels to grayscale in a more controlled, often perceptual way. That typically makes blue render darker relative to red unless you deliberately adjust the color channel mix or apply a virtual color filter.

So yes: your last theory is the correct one. The difference is primarily due to the non-uniform color response of older black-and-white film, sometimes combined with filter use, rather than the flag itself changing color.