While both lr-pcsx_reamrmed and PCSX-ReARMed have an emulated BIOS to fall back on, it has limited compatibility so most games will have issues running with it (or not work at all), and all games that use memory card saves are prone to save corruption. It should be considered mandatory to manually install an official BIOS.
I'm in the same situation as you... I would love to play games like Time Crisis with my DolphinBar and my Wiimote as "the Light Gun" in the DIY Arcade machine that I'm currently building, but... PCSX-Rearmed doesn't detect my Wiimote as "the Light Gun"... Only recognizes standard controls, nothing more... It's very frustrating...
Hope someone could do a simple and easy to follow tutorial on how to make the Light Guns to work with this core, and also make sure that all of the other games still work the same as they do right now with the unmodified core already available from the RetroPie Setup.
Hope that this topic gets more atention.
You could also convert the cue/bin files to one chd file and save some disk space along the way. I explained here how to do it on Retropie or any other Debian-based Linux. Its as easy as copying three comand lines to the console.
I try 3 games Final Fantasy VIII, XI and Metal Gear Solid with CD Access Method (Restart) set to synchronous. All games are with .M3U files and .CDx extentions . I use the new disk control menu.
-All games are booting fine
-I start all games from CD2 and when the game ask for CD1 the changes was succesfully
-I use a save file in FF 8 and when the game ask for CD2 the change was succesfully
-I try 3 times to change the disk without the game ask for this (it's not a normal condition) and i had a lock-up and 2 times a black screen(i choose reset from retroarch to get out from this)
Generally, the fixed version working fine without the previous lock-ups during exit and during disk swapping.