NUPS is the desktop program associated with UPS files on Windows. The utility record lists version 1.4 dated 23 Jan 2023, running on .NET or Mono. It creates a UPS, applies one, and can show the offsets the patch changes. That last part is the reason to install it. The browser applies a UPS and can create one, but it does not give you a scrollable offset list the way NUPS does.
The format itself is UPS1 plus lengths, XOR blocks, and three CRC32 values. NUPS is not a second format. If a readme says NUPS, the file you download is still .ups and the home page can apply it. I install NUPS when I am the person making the patch on Windows or when I want to see which ranges moved. I do not install it merely to play a hack someone else already published.
A source checksum failure inside NUPS means the same thing it means here: the dump is not the one hashed into the trailer. FireRed 1.0 versus 1.1 is the usual GBA example. NUPS will not fix a mismatched base by ignoring the CRC. If a build offers a skip, you are choosing to write a file the author did not hash. I leave that choice in the desktop program and keep this site's explanation on the UPS page.
The old utility page is an archive snapshot, which is why I cite the date carefully. Later builds may exist outside that snapshot. Until I have a second listing, 1.4 on 23 Jan 2023 is the version I will say. Related pages: the UPS format guide and the GBA console guide.