The PCI version of the card cannot adhere to the mechanical part of the PCI spec because the 8 serial connectors are simply too large. If it doesn't fit in your computer, bring back the card. Having a shadow variable would cause an extra memory access on every IO instruction. They don't set the interrupt enable bit. These are used during initialization.
Normal operation uses the old variant which enables the interrupt line.
Gets saved in your config file. If you need this, bug me about it, I'll make it. No bugging needed. I suspect that this is because the CD1864 is not rated for 33MHz operation. Therefore the CD1864 versions of the card can't do 115k2 on all ports just like the CD1865 versions.