Welcome to the most annoying thing regarding SNES mapping! Sadly, there are no magic solution so far regarding this particular problem.
The problem lies with what I think is called the "overscan" color, which should be the first color entry in the background color palette. In very simple terms and as far as I understand, it's basically what appears by default if there's nothing actively displayed.
We've been lucky enough in recent years to see several emulators feature an option to change this color:
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FCEUX for the NES:
You have to open the config file and search for "gNoBGFillColor", then change the number following it to something else, like 100 for a bright pink background.
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Gens with
Maxim's Kmod modifications for the Genesis/Sega CD/32X
Go in the following menus: CPU -> Debug -> Layers and you'll get the option to disable individual layers as well as change the background color.
I also just checked Gens Rerecording and Kega Fusion, and neither allows you to do that.
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VBA-M for the GBA/GB/GBC
I remember getting one of the coders to add the option to change the background color 0 over a year ago. You simply go to the following menus: Tools -> Palette Viewer, then click the "Change backdrop color" button.
As for the SNES, the only option I've found so far is to use
vSNES, a utility which allows you to edit your savestates to view pretty much any information it contains, including the various graphical layers of the screen with any background color you might want. Unfortunately, it only shows the screen that was visible when you saved and a bit more beyond the edges, but that's it. You'd need to save constantly to get everything, making mapping a bit of a chore.
I'll try and look around tonight to see if new tools or emulators came around during the last year to change this sorry state of things. Nope, haven't found anything yet.