I realize that this design will not produce straight lines but I don't really see this as a problem. the objects we place on top of our hexmap do not need to be hex shape they only need to occupy hex space. instead of tring to break the design you need to look at how you can use it to your advantage. and as far as the edge of your map you should create a buffer zone so you can't ever scroll to the edge. I plan to use natural barriers like the stone walls or something like it. I dont plan on using a special shader for this rather display lists of some sort. I will use predfined entrance point to chain maps
together rather then one large map. here are some more examples I found that kind of follow what I have in mind.

http://alumnus.caltech.edu/~leif/FRP/maptiles.html
http://www.terraincraftsman.com/