Is there a significant difference between these files?
I didn't even realize BPS was a thing until seeing it mentioned in this topic. But a quick search led me to the details: expanding on what filler said, the difference between IPS and BPS is user-friendliness. IPS requires the user to know whether their game is headered or not. BPS will patch the correct areas regardless, because it detects and adjusts for headers.
BPS also has no size limitation, whereas an IPS patch tops out at 16 MB. Not really an issue for older games, but it's easily possible for anything NDS and beyond to require more than 16 MB worth of changes.
For all intents and purposes, BPS really ought to replace IPS, since it's essentially the same thing without the limitations.