You are generally discouraged from editing things for ROMs in a conventional graphics editor, though some tile editors/graphics viewers will allow for import and export of BMP. I tend to use crystaltile2 for this but I don't know how it fares for 3ds stuff.
The main problem is most games use palette driven images rather than straight up bitmaps and with it comes colour limitations. The biggest problem for image editors being the reliance of modern ones on blended colours and such like.
You can work around this in several ways. Some just deal with it in their head (if you are only dealing with one colour that needs changing it does not really matter what it is as long as it goes back OK), some export the colours from a tile editor (few will have bitmap import and export but many will export and import windows palettes just fine), some remake them (much like the sort it in your head then you need not have the exact shade as long as it is close enough to do the job)
The problems tend to come when gradients, shadows, highlights and such are used and you have examples of all of those in that. It is not so bad for the top image where you could just copy and paste a segment of the gradient over the text and do whatever you like otherwise. The bottom one though...
You can limit the colours used in an image as well, it tends to be called indexed mode though there might be others.
https://docs.gimp.org/en/gimp-image-convert-indexed.html
https://helpx.adobe.com/photoshop/using/color-modes.html
Technically both will try to make whatever colours you want to use work with the palette you have available (or maybe dither something) but it is not a foolproof thing. I don't see a means to dodge it either (if a quick brown fox... allows you to have every character).
