Yes, your system should be able to run the BeOS.
The design goal is that the BeOS will use the supported graphics card and gracefully ignore the unsupported card. We'll fix any and all bugs we can find that prevent this from working (and we've already found a few).
Note that some graphics cards will actually conflict with each other when installed on the same system (usually when one card is a clone of the other). This is a hardware-level conflict, and we can't fix those, so some graphics card pairs will be unsupportable, even with bug fixes.