If the board is already bricked, you can't brick it much worse than it already is.
File extensions are only a matter of user convenience. The name and extension don't matter as long as the file's content is correct, you just need to override the software's default file extension filter to something that includes whatever the file name you want to load is. For the motherboard I tried to unbrick, the MSI raw binary BIOS files were named *.Nxx and *.Pxx, so making them show up in the CH341 software simply required me to change the file filter to *.N* or *.P*. There is no file format check in the tool, it simply loads the file as-is as a binary blob, no questions asked.
In your case, your BIOS file had some extra metadata that UEFITool had to strip to produce the correct file size. Hopefully it spit out a usable file. You won't know until you try to flash it or de-assemble it to check it for correctness.
In my friend's board's case, what I found out upon attempting to read the board's original SPI chips was that they were corrupted and one of them was outright fried - reads blank and wouldn't take programming.