Assuming I'm correct, the time taking to re-create the schematic on the board would offset the time taken by eagle's quirks.
I seriously doubt that.
If your PCB has more than 2 or 3 components, you need software that ties the schematic to the PCB.
IMO, eagle's "quirks", while real, are easy enough to get used to, and much easier to deal with than trying to make a PCB layout by connecting pins on pads with no logical connections.
-j