Running assembly on the backside would have added about 25% to the cost of production, 4 layer another 25% - so if we wanted to say make the smallest DigiX possible and break arduino layout compatibility we probably could have made it half the size (or perhaps a third more stuff) - but while I think the DigiX is a really good deal for what you get, it still is more than I think a development board should ideally cost (blame it on the Digispark). So making a board that was say $99 (production) and $200 (beta) wasn't really something I was interested in.
The other motivator is I like to keep things easy enough to copy/remix/make for everyday makers - double layer boards with single sided assembly goes with that nicely.
An interesting fact on the DigiX - I spent well over a week trying to get it routed (at all, not just well) on double layer layout (Arduino uses a 4 layer for the due with less on it) - it made me finally try topographical routing (no corners, all flowing lines) and that is the only way I was able to route it, it took several months to clean up the routing (with a few prototypes in there) to get it where it is. That is why if you look at the traces they look crazy and unlike almost any other board.
I'm working on a 4 layer project but it is more in the multiple Ghz range of power.
I think it would be fun, for the sake of fun, to do a double sided assembly Digispark on four layer with a micro usb connector and edge connections for the outputs - I bet I could get it under 1/2" square with the same features - but I haven't had time for projects like that in awhile (baby+day job+business) which is a good thing (success!) but I still hope to retire some day and pursue the fine art of building the small simple USB boards and the like.