Can you change the VBA background?

[Sperbus]

Being able to turn off sprite layers in VisualBoy Advance is so useful, but it's not that useful when the default background is black against something with a black outline (examples provided). Is there any way to change the default background layer for the system? Maybe just change the color?

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It's also different colors in different parts of the game... anyone know why?

[Barack Obama]

Go into Memory Viewer, then in offset select "PALETTE"

At the first column of the 0500000 row, switch from 00 to 10.

Note: this will not work with Game Boy and Game Boy Color games unfortunately.

Source:
https://www.vg-resource.com/thread-31790.html

For your other question:
Different tilesets / maps use different background colours, it's the same for SNES too. Rudra for example uses black almost everywhere, but some maps have something different (green for a forest, grey for a ruined city, etc.).