bflyt files handle UI layouts. It may help you change the title screen's coordinates, or some hardcoded text strings (copyright notices, typically) but it's very unlikely to contain the actual title screen textures. What it IS useful for, however, is that it will have the filenames for those textures (may be a GC era filetype like timg, or a DS/3DS texture or whatever.)
Use a hex editor, or one of the many 3DS modding toolkits.
Yes it does display properly
The game still freezes even with just the 1px change
Codecs, image sizes, file sizes, integrity checks (unlikely but possible and a PITA)