The sounds are a little harsher in fbneo (more high-frequency?)
The sound in FBNeo should be accurate (one of our devs has access to the cabinet). Make sure you are using the right sample file for each emulator, iirc MAME need sample files with the matching samplerates, while that shouldn't be a major problem (apart maybe quality loss) for FBNeo which will convert at runtime if it doesn't match the expected samplerate. You might also want to play around with sound settings in FBNeo's core options if you don't like the default (requires restart). Btw, i'm using that sample with dkong on FBNeo (it's not copyrighted content afaik so it should be ok to share).
The girders are more pink in fbneo
FBNeo has the right colors (iirc the pink is not the only difference), it was fixed around 2011 in MAME and backported to FBAlpha in 2018.