It's going to be difficult to achieve that. For one thing, on the Uno, only one port (D) gives access to 8 bits and even then two are shared with the serial ports. And on other processor what if the user happens to want to use pins that aren't in a single port?
The more hardware-independent approach (using pin numbers rather than hardware ports) is what the IDE currently supports, for good reason.
You can gain a ton of efficiency by using atomic 8-bit operations on a whole PORT instead.
It will be faster. I don't know about quantifying it like that. A bit depends how often you write to the LCD. A panel showing the room temperature, for example, won't matter if it updates a few microseconds faster.
I'm looking for a way to support any current or future MCU (within reason) without having to republish the library with chip-specific layouts when they change, or have the user go and modify library sources because they want to use PORTD instead of B.
The current system attempts to do that, with its table mapping ports (and pins within ports) in a platform-independent way. So that digitalWrite (3, HIGH) works on lots of different processors.
I'm not sure that what you are proposing (rejecting the IDE and then substituting something that achieves the same end-result) is going to be worth the effort.