And, after switching modes, how do you select a different table?
1- You can still make a settings.ini for the header even if it's still BPRE or any of the other defaults. NSE checks the settings.ini file before checking its internal resources for information.
2- If by selecting a different table you mean, the one that points to all the Sprites (aka Overworlds), then just add a property to your settings file with the offset.
//Example using the original header BPRE
Start palette = &H700000
Sprite table = &H39fdb0