In RuinHandler.java (line 292 I think) you go through all BiomeGenBase biomes, 
but stop as soon as one of them is null. There's a gap between default biome 
IDs and ExtraBiomesXL IDs (for me, last default biome is 22, first ebxl is 32). 
So there's no way to specify chances for ebxl biomes...

Apparently I'm too stupid to come up with any sort of solution for this, so I 
hope you can find something and even want to. Something tells me this is 
ExtraBiomesXL doing it wrong with biome IDs...