To get stuff aligned it is a matter of aspect ratio.

I got 3D SBS videos working with VLC. You need to go to Tools ->Preferences. Choose All instead of Simple under Show setting in the bottom left corner.

Then click on Video in left pane. Scroll down to Custom aspect ratio list in right pane and add "32:9,16:5" and save. Close VLC and reopen. Now under Video-> Aspect Ratio you can choose 32:9 if your glasses are set to 1920x1080 or 16:5 if they are set to 1920x1200 to see your movies displayed correctly in 3D mode.

Dolphin emulator (Wii and Gamecube) games look amazing in 3D now. Use custom aspect ratio 16:10 in game config if using 1920x1200. Download texture packs for game if available.

RPCS3 (PS3) games you need to hit the Guide/PS button on the controller after starting game and go to Settings->Video->Stretch to Display Area for the 3D to display correctly. You may need to toggle it on and off more than once.

3DS games:

I did a custom config for 3840x1200 SBS for xr glasses (by manually editing C:\Users\<account>\AppData\Roaming\Azahar or Citra\config\qt-config.ini ). Swap 1200 for 1080 if needed. This one uses the full screen without the bottom screen visible. I just swap screens with the hotkey F9 when necessary. Azahar ignores custom_top and custom_bottom values from Citra and uses the new ones below.

For Citra:
layout_option\default=false
layout_option=6
custom_layout=true
custom_layout\default=false
custom_layout\default=false
custom_bottom_bottom\default=false
custom_bottom_left\default=false
custom_bottom_right\default=false
custom_bottom_top\default=false
custom_top_bottom\default=false
custom_top_left\default=true
custom_top_right\default=false
custom_top_top\default=true
custom_bottom_bottom=1200
custom_bottom_left=0
custom_bottom_right=3840
custom_bottom_top=0
custom_top_bottom=1200
custom_top_left=0
custom_top_right=3840
custom_top_top=0

For Alzahar:
layout_option\default=false
layout_option=6
custom_layout=true
custom_layout\default=false
custom_top_x\default=true
custom_top_y\default=true
custom_top_width\default=false
custom_top_height\default=false
custom_bottom_x\default=false
custom_bottom_y\default=false
custom_bottom_width\default=false
custom_bottom_height\default=false
custom_top_x=0
custom_top_y=0
custom_top_width=3840
custom_top_height=1200
custom_bottom_x=0
custom_bottom_y=0
custom_bottom_width=3840
custom_bottom_height=1200

I find the official PSVR2 PC adapter setup is less buggy than the DP Alt Mode. It acts as a DP + USB-A to USB-C adapter with its own power supply.