I've used the map-creation tool WorldPainter to create a custom-map. It pre-generates the chunks, whilst leaving the population to minecraft itself.

From the WorldPainter Wiki

When Minecraft generates land, it does so in two steps:

In step one, it calculates the biomes according to its own world generating algorithm and then generates the actual land mass, surface terrain (grass, sand, etc.), river or ocean water and caves. Since WorldPainter pre-generates the chunks, Minecraft never performs this step for those chunks.

In step two, the "populate" step, Minecraft adds underground resources (ores, lava and water lakes), creates the vegetation (trees, tall grass, mushrooms, flowers, lily pads, etc.), small lava and water lakes on the surface and structures (abandoned mines, NPC villages, strongholds, dungeons and desert and jungle temples). It does this according to the biome settings stored in the chunk. This second step can be performed by Minecraft on chunks generated by WorldPainter, because there is a flag for each chunk in the map data telling Minecraft whether that chunk has been populated yet.

As this map is rather large (30k by 30k) i'd love to be able to pre-populate it, as the population phase can still induce a significant strain on the server with mods installed.
I've tried to use the "force" method of filling to populate, it seems to have no affect whatsoever (i re-ran the dynmap render to see).

I hope you can add support for pre-population :)

WorldBorder is only specifically compatible with world generation plugins which are registered through Bukkit, as it uses Bukkit's chunk loading/generation methods. Mods external to Bukkit (through MCPC or whatever) as a rule of thumb won't work properly with Fill. Sorry.

The "populate" step as they put it is handled by the Fill process, done by loading adjacent chunks to trigger that. Your problem would be as above.