I had success using both cards at the same time without any "Recoverable Alert" now, while playing around and creating some kind of multiboot workbench-setup for a real-A1200/winuae/amithlon installation.
For this to work I ended up with individual p96mode_settings-files again. If done correctly and every monitor has it's own p96mode_settings, it is possible to have all resolutions shown in screenmode prefs as well, but you need to make sure, the settings have been attached to the board indiviually. So having all the settings in one single file is *not* necessary for this to work at all. Additionally it is very troublesome, if you attach settings to your boards and remove one of the boards later on. Then there is a mis-assignment between gfx-board and p96mode prefs, because it "attaches" its settings to boards by index number!
E.g.: If board #0 is a radeon and board #1 is a voodoo and you remove the radeon, the voodoo is board #0 now and these settings (actually fitting the radeon) will be used for the voodoo3, which leads to problem as you can imagine. I wonder why p96mode prefs is that "dumb" ?! Is there a way to make it actually look up what type/kind of board is available and use matching settings instead of simply applying settings by index and counting the number of boards in the system ?! You could not even swap pci-ports of the gfx boards, the p96mode settings won't match anymore.
Well, to make a long story short, for multiboot systems, it seems best to attach settings to boards only, when they are the only one in the system, so every board has it settings attached to board #0. You can only use the first board in the system then, that's a drawback but you gain kind of plug-n-play feature.. o) Remove any board and the next one takes over automatically, because its settings have been attached to index #0 as well. You need to make sure to load only the one and only fitting monitor-driver for this to work of course (I use "showboards" to detect which gfx board is available and run that monitor-driver eventually).